title: Htr3a_tdTpositive_cell_92

value: single cell

value: Vip Gpc3


title: Htr3a_tdTpositive_cell_71

status: Public on Jan 04 2016

type: SRA

city: Seattle

first: Lucas

middle: T

last: Gray

state: WA

address: 615 Westlake Ave N

department: Molecular Genetics

country: USA

institute: Allen Institute for Brain Science

library_source: transcriptomic

data_processing:
Adapter sequences were clipped from 100 base-pair single-end reads in FASTQ format using the ea-utils application fastq-mcf with settings -C 200000 to filter against Nextera adapter sequences.
Trimmed reads were aligned to GRCm38 (mm10) using the RefSeq annotation gff file downloaded on 6/1/2013. Transcriptome alignment files in BAM format were generated with RSEM v1.2.4 and Bowtie v1.1.0 using the program rsem-calculate-expression with settings --keep-intermediate-files --bowtie-chunkmbs 2000 --output-genome-bam --bowtie-e 500 --bowtie-m 100.
Reads that did not map to the RefSeq annotations were aligned to ERCC sequences and tdTomato sequence using Bowtie v1.1.0 with settings -S --chunkmbs 2000.
Genome_build: mm10
Supplementary_files_format_and_content: CSV: Comma-separated tables of data values; Columns are samples and Rows are genes or ERCC/tdTomato. Column names correspond to sample Titles; Row names correspond to RefSeq Gene Symbols, ERCC symbols, or tdTomato.

molecule: total RNA

organism: Mus musculus

source_name: Primary visual cortex

growth_protocol: Animals were provided food and water ad libitum and were maintained at a regular 12 h day/night cycle at no more than 5 adult animals per cage. Animals were maintained on the C57BL/6J background.

extract_protocol:
Individual adult male mice (P56±3) were anesthetized in an isoflurane chamber, decapitated, and the brain was immediately removed and submerged in fresh ice-cold artificial cerebrospinal fluid (ACSF). The brain was sectioned on a vibratome (Leica VT1000S) on ice, and each slice (300-400 µm) was immediately transferred to an ACSF bath at room temperature. After the brain slicing is complete (not more than 15 minutes), individual slices of interest were transferred to a small Petri dish containing bubbled room temperature ACSF. The regions of interest (all layers of VISp or specific layers of VISp) were microdissected under a fluorescence dissecting microscope, and the slices before and after dissection were imaged to later examine the location of the microdissected tissue and confirm its location within V1. The dissected tissue pieces were transferred to a microcentrifuge tube and treated with 1 mg/ml pronase in carbogen-bubbled ACSF for 70 minutes at room temperature without mixing in a closed tube. After incubation, with the tissue pieces sitting at the bottom of the tube, the pronase solution was pipetted out of the tube and exchanged with cold ACSF containing 1% fetal bovine serum. The tissue pieces were dissociated into single cells by gentle trituration through Pasteur pipettes with polished tips of 600, 300, and 150-µm diameter. Single cells were isolated by FACS into individual wells of 96-well plates or 8-well PCR strips containing 2.275 µl of Dilution Buffer (SMARTer Ultra Low RNA Kit for Illumina Sequencing, Clontech Cat#634936), 0.125 µl RNase inhibitor (SMARTer kit), and 0.1 µl of 1:1,000,000 diluted RNA spike-in RNAs (ERCC RNA Spike-In Mix 1, Life Technologies Cat#4456740). Sorting was performed on a BD FACSAriaII SORP using a 130um nozzle, a sheath pressure of 10psi, and in the single cell sorting mode. To exclude dead cells, DAPI (DAPI*2HCl, Life Technologies Cat#D1306) was added to the single cell suspension to the final concentration of 2 ng/ml. FACS populations were chosen to select cells with low DAPI and high tdTomato (tdT) fluorescence. In some cases, we also selected cells that have low DAPI and low tdT fluorescence, in order to capture tdT-negative cells from a sample. To collect all cells in an unbiased manner, we selected all cells with low DAPI fluorescence, regardless of their tdT fluorescence level. Sorted cells were frozen immediately on dry ice and stored at -80°C.
We used the SMARTer kit from Clontech (SMARTer Ultra Low RNA Kit for Illumina Sequencing, Clontech Cat#634936)  to reverse transcribe single cell RNA, and amplify the cDNA for 19 PCR cycles. To stabilize the RNA after quickly thawing the cells on ice, we immediately added to each sample an additional 0.125 µl of RNase inhibitor mixed with SMART CDS Primer II A. All steps downstream were carried out according to the manufacturer’s instructions. Each amplification experiment included a set of controls: 10 pg cortex RNA (isolated from Rbp4-Cre;Ai14, P57 male) as positive control for amplification, ERCC-only control to demonstrate the absence of RNases throughout the sorting process, and water-only control, to control for specificity of amplification/absence of contamination. cDNA concentration was quantified using Agilent Bioanalyzer High Sensitivity DNA chips. For most samples, 1 ng of amplified cDNA was used as input to make sequencing libraries with Nextera XT DNA kit (Illumina Cat#FC-131-1096). For smaller cells (e.g., glia), which did not consistently produce more than 1ng cDNA, we used 0.5–1 ng cDNA as input.  We stopped the procedure after PCR clean-up and did not perform library normalization or library pooling. Individual libraries were quantified using Agilent Bioanalyzer DNA 7500 chips. In order to assess sample quality and adjust the concentrations of libraries for multiplexing on HiSeq, all libraries were sequenced first on Illumina MiSeq to obtain approximately 100,000 reads per library, and then on Illumina HiSeq 2000 or 2500 to generate 100 bp reads.

tag: mouse line abbreviation

tag: driver 1

tag: reporter

value: RCL-tdT (Ai14)

tag: brain region

value: VISp

tag: dissection

value: upper

tag: input material

tag: tdtomato labelling

value: positive

tag: passes qc checks

value: Y

tag: primary type

value: L6a Plcxd3

tag: secondary type

value: Pvalb Gpx3

tag: allen science vignette cell id


title: Htr3a_tdTpositive_cell_62

value: Vip Cxcl14_Car4

value: Vip Chat


title: Nos1_tdTpositive_cell_38

value: All

value: L6 Syt17

value: L5a Syt17


title: Nos1_tdTpositive_cell_37


title: Nkx2-1_tdTpositive_cell_8

value: Pvalb Cpne5


title: Nos1_tdTpositive_cell_35

value: Sst Chodl


title: Htr3a_tdTpositive_cell_56

value: Vip Mybpc1


title: Nos1_tdTpositive_cell_34

value: single cell


title: Htr3a_tdTpositive_cell_55

value: Ndnf Car4

value: Ndnf Cxcl14


title: Htr3a_tdTpositive_cell_4

value: RCL-tdT (Ai14)

value: VISp


title: Nos1_tdTpositive_cell_32

value: positive


title: Htr3a_tdTpositive_cell_15

value: Y


title: Nos1_tdTpositive_cell_31

value: Igtp


title: Gad2_tdTpositive_cell_80

value: N


title: Gad2_tdTpositive_cell_79


title: Nos1_tdTpositive_cell_29


title: Gad2_tdTpositive_cell_78


title: Nos1_tdTpositive_cell_28

value: L5a Batf3


title: Nos1_tdTpositive_cell_27

value: L5a Fam5c


title: Gad2_tdTpositive_cell_76

value: All


title: Gad2_tdTpositive_cell_77

value: OPC/Oligo


title: Gad2_tdTpositive_cell_75

value: Pvalb Wt1


title: Htr3a_tdTpositive_cell_101

value: L6b Trh


title: Nos1_tdTpositive_cell_26

value: L5a Syt17


title: Gad2_tdTpositive_cell_74

value: Pvalb Cpne5


title: Nos1_tdTpositive_cell_36

value: single cell


title: Gad2_tdTpositive_cell_73


title: Nos1_tdTpositive_cell_24

value: Sst Chodl


title: Nos1_tdTpositive_cell_23

value: L2/3 Otof


title: Gad2_tdTpositive_cell_71

value: RCL-tdT (Ai14)

value: Pvalb Tpbg


title: Nos1_tdTpositive_cell_33

value: VISp

value: positive


title: Gad2_tdTpositive_cell_70

value: Y

value: Vip Sncg


title: Nos1_tdTpositive_cell_21


title: Nos1_tdTpositive_cell_20


title: Nos1_tdTpositive_cell_19

value: Ndnf Car4


title: Gad2_tdTpositive_cell_69


title: Gad2_tdTpositive_cell_68

value: Sst Cbln4


title: Nos1_tdTpositive_cell_30

value: All

value: L5a Batf3


title: Gad2_tdTpositive_cell_66


title: Nos1_tdTpositive_cell_18


title: Gad2_tdTpositive_cell_65

value: Pvalb Tacr3


title: Gad2_tdTpositive_cell_64


title: Gad2_tdTpositive_cell_63

value: Vip Gpc3


title: Nos1_tdTpositive_cell_14


title: Ntsr1_tdTpositive_cell_41

value: L6a Mgp


title: Nos1_tdTpositive_cell_25


title: Nos1_tdTpositive_cell_16


title: Gad2_tdTpositive_cell_72

value: Sst Myh8


title: Nos1_tdTpositive_cell_12

value: single cell


title: Gad2_tdTpositive_cell_62


title: Nos1_tdTpositive_cell_15

value: Sst Chodl


title: Nos1_tdTpositive_cell_13

value: Igtp


title: Gad2_tdTpositive_cell_60

value: RCL-tdT (Ai14)

value: Vip Chat


title: Nos1_tdTpositive_cell_22

value: VISp


title: Gad2_tdTpositive_cell_61

value: positive

value: Pvalb Gpx3


title: Nos1_tdTpositive_cell_10

value: Y


title: Gad2_tdTpositive_cell_59

value: Ndnf Cxcl14


title: Nos1_tdTpositive_cell_11


title: Gad2_tdTpositive_cell_58


title: Gad2_tdTpositive_cell_57

value: Pvalb Tpbg


title: Nos1_tdTpositive_cell_9

value: All


title: Gad2_tdTpositive_cell_67


title: Nos1_tdTpositive_cell_6


title: Ndnf_tdTnegative_cell_12

value: Ndnf

value: negative


title: Nos1_tdTpositive_cell_7


title: Nos1_tdTpositive_cell_17


title: Gad2_tdTpositive_cell_55

value: Pvalb Wt1

value: Pvalb Rspo2


title: Ndnf_tdTnegative_cell_11

value: Endo Myl9


title: Gad2_tdTpositive_cell_54

value: single cell


title: Gad2_tdTpositive_cell_53

value: Ndnf Car4


title: Gad2_tdTpositive_cell_52

value: Vip Gpc3


title: Ndnf_tdTnegative_cell_10

value: RCL-tdT (Ai14)

value: Astro Gja1


title: Ndnf_tdTnegative_cell_9

value: VISp

value: L2 Ngb


title: Gad2_tdTpositive_cell_50

value: positive

value: L2/3 Otof


title: Ndnf_tdTnegative_cell_8

value: Y


title: Ndnf_tdTnegative_cell_7


title: Gad2_tdTpositive_cell_51


title: Gad2_tdTpositive_cell_49


title: Gad2_tdTpositive_cell_47


title: Ndnf_tdTnegative_cell_4


title: Ndnf_tdTnegative_cell_3


title: Gad2_tdTpositive_cell_48


title: Ndnf_tdTnegative_cell_6


title: Gad2_tdTpositive_cell_43


title: Ndnf_tdTnegative_cell_5


title: Gad2_tdTpositive_cell_42


title: Gad2_tdTpositive_cell_56

value: Ndnf Cxcl14


title: Ndnf_tdTnegative_cell_1


title: Ndnf_tdTpositive_cell_21

value: All

value: N


title: Ndnf_tdTnegative_cell_2

value: Ndnf

value: negative

value: Sst Cbln4


title: Gad2_tdTpositive_cell_41


title: Gad2_tdTpositive_cell_40


title: Ndnf_tdTpositive_cell_20


title: Gad2_tdTpositive_cell_37


title: Gad2_tdTpositive_cell_39


title: Gad2_tdTpositive_cell_38

value: Vip Chat


title: Ndnf_tdTpositive_cell_18

value: single cell


title: Gad2_tdTpositive_cell_36


title: Ndnf_tdTpositive_cell_17


title: Ndnf_tdTpositive_cell_16

value: Ndnf Car4


title: Gad2_tdTpositive_cell_35


title: Gad2_tdTpositive_cell_33

value: Vip Gpc3


title: Gad2_tdTpositive_cell_32

value: RCL-tdT (Ai14)

value: Vip Cxcl14_Car4


title: Ndnf_tdTpositive_cell_15

value: VISp


title: Ndnf_tdTpositive_cell_14


title: Ndnf_tdTpositive_cell_13


title: Ndnf_tdTpositive_cell_11

value: Endo Tbc1d4


title: Gad2_tdTpositive_cell_34

value: positive

value: Vip Mybpc1


title: Gad2_tdTpositive_cell_31

value: Y

value: Sncg


title: Gad2_tdTpositive_cell_30

value: All

value: Astro Gja1


title: Ndnf_tdTpositive_cell_10

value: Ndnf


title: Gad2_tdTpositive_cell_29


title: Gad2_tdTpositive_cell_28

value: Pvalb Cpne5


title: Ndnf_tdTpositive_cell_12


title: Ndnf_tdTpositive_cell_9


title: Ndnf_tdTpositive_cell_5

value: Endo Myl9


title: Ndnf_tdTpositive_cell_4


title: Ndnf_tdTpositive_cell_7


title: Gad2_tdTpositive_cell_27

value: Igtp


title: Gad2_tdTpositive_cell_24

value: single cell


title: Gad2_tdTpositive_cell_25


title: Gad2_tdTpositive_cell_26

value: Ndnf Cxcl14


title: Gad2_tdTpositive_cell_23

value: Vip Chat

value: Vip Gpc3


title: Gad2_tdTpositive_cell_22

value: RCL-tdT (Ai14)

value: Vip Sncg


title: Ndnf_tdTpositive_cell_3

value: VISp

value: Endo Tbc1d4


title: Gad2_tdTpositive_cell_21

value: positive

value: Vip Cxcl14_Car4


title: Ndnf_tdTpositive_cell_2

value: Y

value: L6 Syt17


title: Gad2_tdTpositive_cell_20

value: All

value: Ndnf Car4


title: Ndnf_tdTpositive_cell_1

value: Ndnf


title: Htr3a_tdTpositive_cell_123

value: L6b Trh


title: Htr3a_tdTpositive_cell_122

value: Sncg


title: Gad2_tdTpositive_cell_19

value: single cell


title: Ndnf_tdTpositive_cell_8


title: Gad2_tdTpositive_cell_17

value: Sst Cbln4


title: Gad2_tdTpositive_cell_15

value: Vip Mybpc1


title: Gad2_tdTpositive_cell_18


title: Htr3a_tdTpositive_cell_120


title: Ndnf_tdTpositive_cell_6

value: Endo Myl9


title: Htr3a_tdTpositive_cell_119

value: RCL-tdT (Ai14)


title: Htr3a_tdTpositive_cell_118

value: Pvalb Cpne5


title: Htr3a_tdTpositive_cell_117

value: VISp

value: L6b Mup5


title: Cux2_tdTpositive_cell_124

value: positive

value: N


title: Cux2_tdTpositive_cell_122

value: Y

value: L2/3 Otof


title: Htr3a_tdTpositive_cell_116


title: Htr3a_tdTpositive_cell_115


title: Cux2_tdTpositive_cell_121


title: Ndnf_tdTpositive_cell_19


title: Htr3a_tdTpositive_cell_114

value: L6a Plcxd3


title: Cux2_tdTpositive_cell_120


title: Cux2_tdTpositive_cell_119


title: Htr3a_tdTpositive_cell_113


title: Htr3a_tdTpositive_cell_112


title: Cux2_tdTpositive_cell_117


title: Htr3a_tdTpositive_cell_111


title: Htr3a_tdTpositive_cell_121


title: Gad2_tdTpositive_cell_14

value: All

value: Vip Chat


title: Cux2_tdTpositive_cell_115


title: Htr3a_tdTpositive_cell_109


title: Htr3a_tdTpositive_cell_108

value: L6b Trh


title: Htr3a_tdTpositive_cell_107


title: Cux2_tdTpositive_cell_116


title: Cux2_tdTpositive_cell_96


title: Cux2_tdTpositive_cell_98


title: Htr3a_tdTpositive_cell_106


title: Htr3a_tdTpositive_cell_105


title: Cux2_tdTpositive_cell_123


title: Cux2_tdTpositive_cell_95


title: Cux2_tdTpositive_cell_97


title: Cux2_tdTpositive_cell_94

value: L2 Ngb


title: Htr3a_tdTpositive_cell_104

value: single cell


title: Htr3a_tdTpositive_cell_102

value: Vip Gpc3


title: Cux2_tdTpositive_cell_91

value: L4 Sparcl1


title: Cux2_tdTpositive_cell_118


title: Cux2_tdTpositive_cell_92


title: Htr3a_tdTpositive_cell_100


title: Cux2_tdTpositive_cell_90


title: Htr3a_tdTpositive_cell_99


title: Htr3a_tdTpositive_cell_110


title: Cux2_tdTpositive_cell_88


title: Htr3a_tdTpositive_cell_98


title: Htr3a_tdTpositive_cell_97


title: Cux2_tdTpositive_cell_87

value: Ndnf Car4


title: Htr3a_tdTpositive_cell_96

value: RCL-tdT (Ai14)


title: Cux2_tdTpositive_cell_86


title: Htr3a_tdTpositive_cell_94

value: lower

value: Sst Tacstd2


title: Htr3a_tdTpositive_cell_91

value: VISp

value: Sst Th


title: Htr3a_tdTpositive_cell_93

value: positive


title: Cux2_tdTpositive_cell_84

value: Y


title: Cux2_tdTpositive_cell_85

value: L5 Hsd11b1

value: L4 Arf5


title: Cux2_tdTpositive_cell_93

value: All


title: Cux2_tdTpositive_cell_83


title: Htr3a_tdTpositive_cell_90

value: Sncg


title: Htr3a_tdTpositive_cell_103

value: Vip Sncg


title: Cux2_tdTpositive_cell_81

value: L2/3 Otof


title: Htr3a_tdTpositive_cell_89

value: single cell


title: Cux2_tdTpositive_cell_82


title: Htr3a_tdTpositive_cell_88

value: Vip Chat


title: Cux2_tdTpositive_cell_89

value: L4 Sparcl1


title: Cux2_tdTpositive_cell_79


title: Htr3a_tdTpositive_cell_85

value: Pvalb Tacr3

value: Pvalb Gpx3


title: Cux2_tdTpositive_cell_77

value: RCL-tdT (Ai14)


title: Cux2_tdTpositive_cell_78


title: Htr3a_tdTpositive_cell_86

value: lower

value: L5a Batf3

value: L6a Plcxd3


title: Htr3a_tdTpositive_cell_84

value: VISp

value: positive

value: Sst Cbln4


title: Cux2_tdTpositive_cell_76

value: Y

value: L4 Scnn1a


title: Cux2_tdTpositive_cell_75

value: All

value: L5a Fam5c


title: Htr3a_tdTpositive_cell_82

value: Sst Tacstd2


title: Cux2_tdTpositive_cell_74

value: single cell


title: Htr3a_tdTpositive_cell_83

value: Sst Th


title: Cux2_tdTpositive_cell_73

value: L4 Sparcl1


title: Htr3a_tdTpositive_cell_80

value: Vip Gpc3


title: Cux2_tdTpositive_cell_71

value: L2/3 Otof


title: Htr3a_tdTpositive_cell_79

value: RCL-tdT (Ai14)

value: L6b Trh


title: Htr3a_tdTpositive_cell_78

value: lower


title: Htr3a_tdTpositive_cell_81

value: Ndnf Cxcl14


title: Cux2_tdTpositive_cell_66

value: VISp


title: Cux2_tdTpositive_cell_61

value: positive


title: Cux2_tdTpositive_cell_62


title: Htr3a_tdTpositive_cell_87


title: Htr3a_tdTpositive_cell_75


title: Htr3a_tdTpositive_cell_77


title: Cux2_tdTpositive_cell_65


title: Cux2_tdTpositive_cell_60


title: Htr3a_tdTpositive_cell_76

value: Vip Mybpc1


title: Htr3a_tdTpositive_cell_74

value: Y

value: Vip Cxcl14_Car4


title: Cux2_tdTpositive_cell_57


title: Cux2_tdTpositive_cell_59


title: Htr3a_tdTpositive_cell_72

value: L6b Mup5


title: Htr3a_tdTpositive_cell_73


title: Cux2_tdTpositive_cell_56


title: Htr3a_tdTpositive_cell_69

value: upper


title: Cux2_tdTpositive_cell_54


title: Cux2_tdTpositive_cell_55


title: Htr3a_tdTpositive_cell_70


title: Cux2_tdTpositive_cell_52


title: Htr3a_tdTpositive_cell_68


title: Htr3a_tdTpositive_cell_67


title: Cux2_tdTpositive_cell_51

value: L4 Scnn1a


title: Htr3a_tdTpositive_cell_66

value: single cell


title: Cux2_tdTpositive_cell_50


title: Htr3a_tdTpositive_cell_65


title: Cux2_tdTpositive_cell_49

value: L2 Ngb


title: Chrna2_tdTpositive_cell_84

value: All

value: Pvalb Gpx3


title: Htr3a_tdTpositive_cell_64

value: Ndnf Car4


title: Htr3a_tdTpositive_cell_63

value: RCL-tdT (Ai14)


title: Chrna2_tdTpositive_cell_83

value: Sst Cdk6


title: Chrna2_tdTpositive_cell_82

value: L5a Batf3


title: Htr3a_tdTpositive_cell_60

value: Ndnf Cxcl14


title: Htr3a_tdTpositive_cell_61

value: VISp


title: Chrna2_tdTpositive_cell_81

value: positive

value: Vip Gpc3


title: Chrna2_tdTpositive_cell_80

value: Y


title: Htr3a_tdTpositive_cell_58


title: Chrna2_tdTpositive_cell_79


title: Chrna2_tdTpositive_cell_77

value: Sst Chodl


title: Htr3a_tdTpositive_cell_57

value: Vip Chat


title: Chrna2_tdTpositive_cell_76


title: Htr3a_tdTpositive_cell_53

value: upper


title: Htr3a_tdTpositive_cell_54

value: Vip Cxcl14_Car4

value: Vip Mybpc1


title: Chrna2_tdTpositive_cell_75

value: single cell

value: L6a Mgp


title: Htr3a_tdTpositive_cell_50


title: Htr3a_tdTpositive_cell_51


title: Htr3a_tdTpositive_cell_49

value: Vip Sncg


title: Chrna2_tdTpositive_cell_72

value: All

value: L5a Syt17


title: Htr3a_tdTpositive_cell_48

value: RCL-tdT (Ai14)


title: Chrna2_tdTpositive_cell_71


title: Htr3a_tdTpositive_cell_47


title: Chrna2_tdTpositive_cell_70

value: Sst Myh8


title: Htr3a_tdTpositive_cell_46

value: Ndnf Cxcl14


title: Chrna2_tdTpositive_cell_69

value: VISp


title: Htr3a_tdTpositive_cell_59

value: positive


title: Htr3a_tdTpositive_cell_44

value: Ndnf Car4


title: Htr3a_tdTpositive_cell_45

value: Y


title: Chrna2_tdTpositive_cell_68


title: Chrna2_tdTpositive_cell_78


title: Htr3a_tdTpositive_cell_43


title: Chrna2_tdTpositive_cell_67


title: Chrna2_tdTpositive_cell_66

value: Sst Tacstd2


title: Htr3a_tdTpositive_cell_41


title: Chrna2_tdTpositive_cell_65

value: Pvalb Gpx3


title: Htr3a_tdTpositive_cell_42


title: Htr3a_tdTpositive_cell_52

value: upper


title: Chrna2_tdTpositive_cell_64

value: Pvalb Obox3


title: Chrna2_tdTpositive_cell_74

value: L5a Batf3


title: Chrna2_tdTpositive_cell_73

value: single cell


title: Htr3a_tdTpositive_cell_40

value: Vip Chat


title: Chrna2_tdTpositive_cell_55


title: Htr3a_tdTpositive_cell_39

value: Vip Cxcl14_Car4


title: Htr3a_tdTpositive_cell_37

value: All


title: Htr3a_tdTpositive_cell_36

value: Vip Sncg

value: Vip Mybpc1


title: Htr3a_tdTpositive_cell_34

value: RCL-tdT (Ai14)


title: Chrna2_tdTpositive_cell_32

value: Sst Myh8


title: Chrna2_tdTpositive_cell_47

value: VISp


title: Chrna2_tdTpositive_cell_38

value: positive


title: Chrna2_tdTpositive_cell_40


title: Chrna2_tdTpositive_cell_41

value: Sst Th


title: Htr3a_tdTpositive_cell_33

value: Y

value: Ndnf Car4


title: Chrna2_tdTpositive_cell_36


title: Htr3a_tdTpositive_cell_32


title: Chrna2_tdTpositive_cell_31

value: Sst Chodl


title: Htr3a_tdTpositive_cell_31


title: Htr3a_tdTpositive_cell_30


title: Htr3a_tdTpositive_cell_29


title: Chrna2_tdTpositive_cell_29

value: Sst Tacstd2


title: Chrna2_tdTpositive_cell_18


title: Chrna2_tdTpositive_cell_13

value: Pvalb Gpx3


title: Htr3a_tdTpositive_cell_26

value: Ndnf Cxcl14


title: Htr3a_tdTpositive_cell_38

value: single cell


title: Chrna2_tdTpositive_cell_12

value: Sncg


title: Htr3a_tdTpositive_cell_27


title: Chrna2_tdTpositive_cell_11


title: Htr3a_tdTpositive_cell_25

value: Vip Cxcl14_Car4


title: Chrna2_tdTpositive_cell_10


title: Chrna2_tdTpositive_cell_9

value: Sst Cbln4


title: Htr3a_tdTpositive_cell_35

value: All


title: Htr3a_tdTpositive_cell_28


title: Chrna2_tdTpositive_cell_8

value: Vip Gpc3


title: Htr3a_tdTpositive_cell_24

value: RCL-tdT (Ai14)


title: Htr3a_tdTpositive_cell_23


title: Chrna2_tdTpositive_cell_6


title: Chrna2_tdTpositive_cell_5


title: Htr3a_tdTpositive_cell_22


title: Chrna2_tdTpositive_cell_4


title: Htr3a_tdTpositive_cell_21

value: Vip Mybpc1


title: Htr3a_tdTpositive_cell_20

value: VISp

value: Vip Chat


title: Htr3a_tdTpositive_cell_19

value: positive


title: Htr3a_tdTpositive_cell_18

value: Y


title: Chrna2_tdTpositive_cell_1


title: Htr3a_tdTpositive_cell_17

value: Ndnf Car4


title: Calb2_tdTpositive_cell_11


title: Chrna2_tdTpositive_cell_3

value: L5a Batf3


title: Htr3a_tdTpositive_cell_14


title: Htr3a_tdTpositive_cell_16


title: Htr3a_tdTpositive_cell_12


title: Calb2_tdTpositive_cell_3

value: L4 Sparcl1


title: Htr3a_tdTpositive_cell_11


title: Htr3a_tdTpositive_cell_10


title: Nos1_tdTpositive_cell_1

value: Endo Myl9


title: Htr3a_tdTpositive_cell_13


title: Htr3a_tdTpositive_cell_6


title: Htr3a_tdTpositive_cell_9

value: Ndnf Cxcl14


title: Chrna2_tdTpositive_cell_7

value: single cell

value: Sst Myh8


title: Htr3a_tdTpositive_cell_7


title: Chrna2_tdTpositive_cell_2


title: Htr3a_tdTpositive_cell_3


title: Gad2_tdTpositive_cell_45

value: Vip Cxcl14_Car4


title: Gad2_tdTpositive_cell_44

value: Oligo Opalin


title: Gad2_tdTpositive_cell_16

value: All

value: Astro Gja1


title: Gad2_tdTpositive_cell_13

value: RCL-tdT (Ai14)

value: Pvalb Gpx3


title: Gad2_tdTpositive_cell_12

value: VISp

value: OPC/Oligo


title: Gad2_tdTpositive_cell_11

value: positive

value: Pvalb Rspo2


title: Gad2_tdTpositive_cell_9

value: Y

value: Pvalb Cpne5


title: Gad2_tdTpositive_cell_10

value: Vip Gpc3


title: AY_rep3_DEM

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

country: Japan

institute: Tohoku University Graduate School of Medicine

data_processing:
Illumina bcl2fastq v2.15.0 software used for basecalling.
Reads mapped against mouse (mm10) genome using the TopHat application on Illumina BaseSpace.
Differential gene analaysis performed using Cuffdiff v2.1.1 application on Illumina BaseSpace.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each genotype were generated using Cuffdiff.

source_name: peritoneal macrophage

growth_protocol: 7-8 weeks of mice were received an intraperitoneal injection of 4% thioglycolate broth. Four days later, macrophages collected by intraperitoneal lavage were cultured in RPMI 1640 medium containing 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was prepared by using RNeasy Mini Kit (QIAGEN) and 1.5 μg of total RNA was used for further steps. Isolation of poly(A)-tailed RNA and library construction were performed using SureSelect Strand Specific RNA Sample Prep Kit (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For analysis of Nrf2-induced state, the macrophages were treated with 100-μM diethylmaleate (DEM) for 6hours

tag: cell type

value: peritoneal macrophage

tag: genotype

tag: treatment

value: DEM treated


title: Gad2_tdTpositive_cell_7

value: single cell

value: Sncg


title: Gad2_tdTpositive_cell_8

value: Sst Cbln4


title: Htr3a_tdTpositive_cell_8

value: Ndnf Cxcl14


title: AY_rep2_basal

value: basal


title: Gad2_tdTpositive_cell_6

value: All


title: Gad2_tdTpositive_cell_5

value: RCL-tdT (Ai14)

value: Igtp


title: AY_rep3_basal


title: WT_rep3_basal

value: wild type


title: Gad2_tdTpositive_cell_4

value: VISp

value: Pvalb Gpx3


title: WT_rep2_DEM


title: Gad2_tdTpositive_cell_3

value: positive

value: Ndnf Car4


title: Gad2_tdTpositive_cell_2

value: Y


title: Htr3a_tdTpositive_cell_5


title: Gad2_tdTpositive_cell_46

value: Vip Cxcl14_Car4


title: Htr3a_tdTpositive_cell_1


title: Htr3a_tdTpositive_cell_2


title: WT_rep2_basal

value: peritoneal macrophage


title: AY_rep1_DEM

value: DEM treated


title: Cux2_tdTnegative_cell_16

value: single cell

value: negative

value: N


title: Gad2_tdTpositive_cell_1

value: Vip Sncg


title: Cux2_tdTnegative_cell_15

value: Micro Ctss


title: AY_rep1_basal

value: basal


title: WT_rep1_DEM


title: Cux2_tdTnegative_cell_14

value: RCL-tdT (Ai14)

value: L2/3 Otof


title: WT_rep1_basal

value: wild type


title: AY_rep2_DEM


title: Cux2_tdTnegative_cell_13

value: VISp

value: Astro Gja1


title: Cux2_tdTnegative_cell_12


title: Cux2_tdTnegative_cell_11


title: WT_rep3_DEM


title: Cux2_tdTnegative_cell_10

value: Endo Tbc1d4


title: Cux2_tdTnegative_cell_9

value: Pvalb Tacr3


title: Cux2_tdTnegative_cell_8

value: Y


title: P2-_2

city: Manchester

first: Georges

last: Lacaud

address: Wilmslow Road

department: Cancer Research UK Manchester Institute

country: United Kingdom

institute: University of Manchester

data_processing:
Basecall files generated from the NextSeq 500 sequencing run were converted to FASTQ format with Illumina’s bcl2fast v2.14. Lane-wise alignment was performed by bowtie2 v2.21 to GRCm38 reference genome with default parameters. Generated SAM files from bowtie2 alignment were converted to BAM files by samtools v0.1.19. Parameters for samtools SAM to BAM conversion: -q 10 -f 2 -F 268. Resulting lane-wise BAM files from the same sequence library were merged into one BAM file used for downstream analysis. Read counts from BAM files were extracted under the R environment (R v3.1.0) with the package Rsubread v1.16.1. Only genes with at least 1 count per million in at least three samples were retained for differential expression analysis. Count table was loaded to edgeR v3.8.5 and differentially expressed genes between groups were identified by exact test function.
Genome_build: GRCm38
Supplementary_files_format_and_content: PreMegE_Counts.txt: Tab-delimited text file includes raw counts for each Sample.

source_name: Bone marrow Pre-Megakaryocyte/Erythroid progenitor, P2-

extract_protocol:
Mouse bone marrow (from 3 mice per sample) was flushed into DMEM supplemented with 10% Foetal Bovine Serum and stained with fluorescently conjugated antibodies. Pre-Megakaryocytic/Erythroid (PreMegE) progenitor cells were isolated by Fluorescence Activated Cell Sorting and RNA was harvested using the QIAGEN RNeasy Plus Micro Kit.
Indexed PolyA libraries were prepared using 50ng of total RNA and 16 cycles of amplification in the Agilent Sure Select Strand Specific RNA Library Prep kit for Illumina Sequencing (Agilent).

tag: strain/background

tag: tissue

value: adult bone marrow

tag: age

value: 12-16 weeks

value: Runx1 P2-hCD4- PreMegE

value: Runx1 P1-GFP::P2-hCD4/+


title: P2-_3


title: P2+_3

source_name: Bone marrow Pre-Megakaryocyte/Erythroid progenitor, P2+

value: Runx1 P2-hCD4+ PreMegE


title: P2+_2


title: Cux2_tdTnegative_cell_7

tag: mouse line abbreviation

value: single cell

value: negative


title: WT_3

source_name: Bone marrow Pre-Megakaryocyte/Erythroid progenitor, WT

value: PreMegE


title: Cux2_tdTnegative_cell_6

tag: driver 1

value: Micro Ctss


title: Cux2_tdTpositive_cell_80

tag: reporter

value: RCL-tdT (Ai14)

value: All

value: positive

value: L4 Scnn1a

value: L4 Sparcl1


title: P2-_1


title: Cux2_tdTnegative_cell_5

tag: brain region

value: VISp


title: WT_1

value: wild type


title: WT_2


title: Cux2_tdTnegative_cell_4

tag: dissection

value: Y

value: Astro Gja1


title: Cux2_tdTnegative_cell_3

tag: input material


title: Cux2_tdTnegative_cell_2

tag: tdtomato labelling


title: Cux2_tdTnegative_cell_1

tag: passes qc checks

value: Vip Chat


title: Cux2_tdTpositive_cell_114

tag: primary type

value: L2/3 Otof


title: Cux2_tdTpositive_cell_112


title: Cux2_tdTpositive_cell_113


title: Cux2_tdTpositive_cell_111


title: Cux2_tdTpositive_cell_110


title: Cux2_tdTpositive_cell_109


title: Cux2_tdTpositive_cell_107


title: Cux2_tdTpositive_cell_106


title: Cux2_tdTpositive_cell_108

tag: secondary type

value: L2 Ngb


title: Cux2_tdTpositive_cell_105

tag: allen science vignette cell id


title: P2+_1

value: adult bone marrow

value: 12-16 weeks

tag: cell type

value: Runx1 P2-hCD4+ PreMegE

value: Runx1 P1-GFP::P2-hCD4/+


title: Cux2_tdTpositive_cell_104

value: single cell


title: Cux2_tdTpositive_cell_103

value: RCL-tdT (Ai14)


title: Cux2_tdTpositive_cell_102


title: Cux2_tdTpositive_cell_99


title: Cux2_tdTpositive_cell_72

value: Sst Cbln4


title: Cux2_tdTpositive_cell_101

value: positive


title: Cux2_tdTpositive_cell_69


title: Cux2_tdTpositive_cell_68

value: L5a Fam5c


title: Cux2_tdTpositive_cell_70

value: L4 Arf5


title: Cux2_tdTpositive_cell_64

value: VISp

value: L4 Sparcl1


title: Cux2_tdTpositive_cell_67

value: Y


title: Cux2_tdTpositive_cell_100


title: Cux2_tdTpositive_cell_58

value: L4 Scnn1a


title: Cux2_tdTpositive_cell_48

value: L5 Hsd11b1


title: Cux2_tdTpositive_cell_45

value: L2/3 Otof


title: Cux2_tdTpositive_cell_46


title: Cux2_tdTpositive_cell_43


title: Cux2_tdTpositive_cell_63

value: Pvalb Tacr3


title: Cux2_tdTpositive_cell_44


title: Cux2_tdTpositive_cell_42


title: Cux2_tdTpositive_cell_41


title: Cux2_tdTpositive_cell_40


title: Cux2_tdTpositive_cell_39


title: Cux2_tdTpositive_cell_53


title: Cux2_tdTpositive_cell_38


title: Cux2_tdTpositive_cell_37


title: Cux2_tdTpositive_cell_35


title: Cux2_tdTpositive_cell_34


title: Cux2_tdTpositive_cell_33


title: Cux2_tdTpositive_cell_31


title: Cux2_tdTpositive_cell_32


title: Cux2_tdTpositive_cell_29


title: Cux2_tdTpositive_cell_30


title: Cux2_tdTpositive_cell_27


title: Cux2_tdTpositive_cell_25


title: Cux2_tdTpositive_cell_47


title: Cux2_tdTpositive_cell_24


title: Cux2_tdTpositive_cell_26


title: Cux2_tdTpositive_cell_23


title: Cux2_tdTpositive_cell_22


title: Cux2_tdTpositive_cell_20


title: Cux2_tdTpositive_cell_21


title: Cux2_tdTpositive_cell_36


title: Cux2_tdTpositive_cell_17


title: Cux2_tdTpositive_cell_19


title: Cux2_tdTpositive_cell_16


title: Cux2_tdTpositive_cell_12


title: Cux2_tdTpositive_cell_10


title: Cux2_tdTpositive_cell_7


title: Cux2_tdTpositive_cell_13


title: Cux2_tdTpositive_cell_15


title: Cux2_tdTpositive_cell_18


title: Cux2_tdTpositive_cell_9


title: Cux2_tdTpositive_cell_11


title: Cux2_tdTpositive_cell_6


title: Cux2_tdTpositive_cell_4


title: Cux2_tdTpositive_cell_3


title: Cux2_tdTpositive_cell_1


title: Cux2_tdTpositive_cell_8


title: Cux2_tdTpositive_cell_28


title: Ctgf_tdTpositive_cell_24

value: Ctgf

value: N


title: Ctgf_tdTpositive_cell_23

value: L6b Mup5

value: L6a Plcxd3


title: Ctgf_tdTpositive_cell_21

value: single cell


title: Ctgf_tdTpositive_cell_22

value: RCL-tdT (Ai14)

value: L6b Trh


title: Ctgf_tdTpositive_cell_20

value: positive


title: Ctgf_tdTpositive_cell_19


title: Ctgf_tdTpositive_cell_18


title: Ctgf_tdTpositive_cell_17


title: Ctgf_tdTpositive_cell_16


title: Cux2_tdTpositive_cell_14


title: Ctgf_tdTpositive_cell_15


title: Cux2_tdTpositive_cell_5


title: Ctgf_tdTpositive_cell_12


title: Ctgf_tdTpositive_cell_8

value: All

value: Endo Tbc1d4


title: Ctgf_tdTpositive_cell_10

value: VISp

value: Endo Myl9


title: Ctgf_tdTpositive_cell_9

value: Y


title: Ctgf_tdTpositive_cell_7


title: Cux2_tdTpositive_cell_2

value: L4 Sparcl1


title: Ctgf_tdTpositive_cell_3


title: Ctgf_tdTpositive_cell_4


title: Ctgf_tdTpositive_cell_2


title: Ctgf_tdTpositive_cell_1


title: Chrna2_tdTpositive_cell_61

value: Vip Sncg


title: Chrna2_tdTpositive_cell_63

value: L5a Batf3


title: Chrna2_tdTpositive_cell_62

value: Pvalb Wt1

value: Pvalb Rspo2


title: Chrna2_tdTpositive_cell_60

value: Sst Cdk6


title: Chrna2_tdTpositive_cell_59

value: Sst Myh8


title: Chrna2_tdTpositive_cell_58


title: Chrna2_tdTpositive_cell_56


title: Chrna2_tdTpositive_cell_57


title: Chrna2_tdTpositive_cell_54

value: Sst Th


title: Chrna2_tdTpositive_cell_53

value: single cell


title: Chrna2_tdTpositive_cell_51

value: RCL-tdT (Ai14)

value: L5a Syt17


title: Chrna2_tdTpositive_cell_52

value: positive


title: Ctgf_tdTpositive_cell_14

value: Ctgf

value: L6b Mup5


title: Ctgf_tdTpositive_cell_13

value: VISp


title: Ctgf_tdTpositive_cell_11

value: L6b Trh


title: Chrna2_tdTpositive_cell_49

value: All

value: Y


title: Chrna2_tdTpositive_cell_50


title: Chrna2_tdTpositive_cell_48


title: Ctgf_tdTpositive_cell_6

value: Endo Tbc1d4


title: Ctgf_tdTpositive_cell_5


title: Chrna2_tdTpositive_cell_42


title: Chrna2_tdTpositive_cell_39


title: Chrna2_tdTpositive_cell_45


title: Chrna2_tdTpositive_cell_43

value: Pvalb Gpx3


title: Chrna2_tdTpositive_cell_44


title: Chrna2_tdTpositive_cell_37


title: Chrna2_tdTpositive_cell_46


title: Chrna2_tdTpositive_cell_35


title: Chrna2_tdTpositive_cell_33


title: Chrna2_tdTpositive_cell_34


title: Chrna2_tdTpositive_cell_28


title: NT shRNA_2

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped with internal pipeline that employs Tophat2 and STAR
reads were counted using an internal perl script and converted to FPKM using mm9
a value of 2 was added to each FPKM value which was then  log2 transformed.  This log-start transform minimizes variance for low read number genes, creates an intuitive minimum of zero and facilitates statistical testing, performed in STATA MP/11.2
Genome_build: mm9
Supplementary_files_format_and_content: matrix txt file with log2FPKM for each gene symbol  for each sample

source_name: C2C12_NT shRNA

growth_protocol: C2C12 myoblasts were transducted by lentivirus constructs containing MLX-WT, MLX-DN and MLX shRNA sequence with empty vector (EV) and non-targetting shRNA controls.

extract_protocol:
RNA was extracted from C2C12 cultures by Trizol reagent followed by cleanup with Qiagen RNAEasy with DNAse treatment.
Total RNA was polyA enriched and prepared for RNA sequencing with TruSeq stranded mRNA library prep kit (Illumina).

tag: cell line

value: myoblasts

tag: transduced with

value: lentivirus constructs containing non-targetting shRNA control


title: Chrna2_tdTpositive_cell_27

value: Sst Cdk6


title: NT shRNA_3


title: NT shRNA_1


title: Chrna2_tdTpositive_cell_26

value: Sst Myh8


title: Chrna2_tdTpositive_cell_25


title: Chrna2_tdTpositive_cell_22

value: L5a Batf3

value: L5a Fam5c


title: Chrna2_tdTpositive_cell_23

value: RCL-tdT (Ai14)

value: single cell

value: Sst Th


title: MLX DN_3

source_name: C2C12_MLX DN

value: lentivirus constructs containing MLX-DN (dominant negative)


title: MLX DN_2


title: Chrna2_tdTpositive_cell_24

value: positive

value: L5a Syt17


title: Chrna2_tdTpositive_cell_21

value: VISp


title: MLX DN_1


title: Chrna2_tdTpositive_cell_16

value: All


title: Chrna2_tdTpositive_cell_17

value: Y


title: Chrna2_tdTpositive_cell_20


title: Chrna2_tdTpositive_cell_15


title: MCS_3

value: control vector expressing only  GFP


title: Chrna2_tdTpositive_cell_19


title: MCS_2


title: Chrna2_tdTpositive_cell_14


title: MCS_1


title: Chat_tdTpositive_cell_4

value: Chat

value: Chat-IRES-Cre

value: Vip Chat


title: Chrna2_tdTpositive_cell_30


title: Chat_tdTpositive_cell_5


title: MLX WT_3

source_name: C2C12_MLX WT

value: myoblasts

value: lentivirus constructs containing MLX-WT


title: MLX WT_2


title: Chat_tdTpositive_cell_2


title: MLX WT_1


title: Chat_tdTpositive_cell_6


title: Chat_tdTpositive_cell_1


title: Calb2_tdTpositive_cell_64

value: lower

value: Ndnf Cxcl14


title: MLX SHRNA_3

source_name: C2C12_MLX SHRNA

value: lentivirus constructs containing MLX shRNA sequence


title: MLX SHRNA_2


title: MLX SHRNA_1


title: Chat_tdTpositive_cell_3

value: RCL-tdT (Ai14)

value: single cell


title: Calb2_tdTpositive_cell_62


title: Calb2_tdTpositive_cell_63


title: Calb2_tdTpositive_cell_56

value: Vip Cxcl14_Car4


title: Calb2_tdTpositive_cell_60

value: positive

value: Vip Mybpc1


title: Calb2_tdTpositive_cell_57

value: VISp


title: Calb2_tdTpositive_cell_58

value: Astro Gja1


title: Calb2_tdTpositive_cell_59

value: Y


title: Calb2_tdTpositive_cell_54


title: Calb2_tdTpositive_cell_61

value: Endo Myl9

value: OPC Pdgfra


title: Calb2_tdTpositive_cell_55


title: Calb2_tdTpositive_cell_52


title: Calb2_tdTpositive_cell_51

value: L2/3 Otof

value: L4 Sparcl1


title: Calb2_tdTpositive_cell_50


title: Calb2_tdTpositive_cell_48

value: upper


title: Calb2_tdTpositive_cell_46


title: Calb2_tdTpositive_cell_47


title: Calb2_tdTpositive_cell_44

value: Vip Gpc3


title: Calb2_tdTpositive_cell_42


title: Calb2_tdTpositive_cell_43


title: Calb2_tdTpositive_cell_38


title: Calb2_tdTpositive_cell_40


title: Calb2_tdTpositive_cell_45

value: L4 Scnn1a


title: Calb2_tdTpositive_cell_36

value: Ndnf Cxcl14


title: Calb2_tdTpositive_cell_39


title: Calb2_tdTpositive_cell_35

value: Vip Chat


title: Calb2_tdTpositive_cell_37

value: RCL-tdT (Ai14)


title: Calb2_tdTpositive_cell_32

value: All

value: single cell


title: Calb2_tdTpositive_cell_53

value: lower

value: positive


title: Calb2_tdTpositive_cell_31

value: VISp


title: Calb2_tdTpositive_cell_27

value: L5a Batf3

value: L6a Plcxd3


title: Calb2_tdTpositive_cell_28

value: Y

value: Endo Myl9


title: Calb2_tdTpositive_cell_26


title: Calb2_tdTpositive_cell_29


title: Calb2_tdTpositive_cell_49


title: Calb2_tdTpositive_cell_23


title: Calb2_tdTpositive_cell_20


title: Calb2_tdTpositive_cell_22

value: Vip Sncg


title: Calb2_tdTpositive_cell_19


title: Calb2_tdTpositive_cell_21


title: Calb2_tdTpositive_cell_30

value: L2 Ngb


title: Calb2_tdTpositive_cell_18


title: Calb2_tdTpositive_cell_41

value: upper

value: Ndnf Car4


title: Calb2_tdTpositive_cell_14

value: L2/3 Otof


title: Calb2_tdTpositive_cell_15

value: Vip Cxcl14_Car4


title: Calb2_tdTpositive_cell_12


title: Calb2_tdTpositive_cell_34

value: Ndnf Cxcl14


title: Nup98HoxA9 ES LMB-treated / anti-FLAG_ChIP

city: Ibaraki

first: Masahiro

last: Oka

state: Osaka

address: 7-6-8 Saito-Asagi

institute: National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN)

library_source: genomic

data_processing:
illumina HCS2.0.5
ChIP-seq reads were aligned with the mouse reference geneme (mm9) using the bowtie program (v1.12.7) with the following parameters: -m 1 -v 3.
Duplicate reads were removed using samtools  (v0.1.18).
The normalized ChIP-seq signal was calculated by　subtracting the Reads Per Million mapped reads (RPM) of the Input signal from the IPed signal.
The signals were calculated at "window-size" bp genomic intervals with "step-size" bp window (e.g., The file name preffix of "w10000s1000" in our processed data means that the window-size is 10,000 bp and the step-size is 1,000 bp. )
genome build: mm9
processed data files format and content: bigWig files were generated for processed data containing chromosome, regions

molecule: genomic DNA

source_name: EB3-derived Nup98-HoxA9 Expressing Stable cell line

extract_protocol:
The cross-linked chromatin was sheared by sonication, and MNase treatment.
To repair ChIP-DNA and Input-DNA ends, T4 DNA polymerase, Klenow enzyme and T4 polynucleotide kinase were used (New England Biolabs), and an A base was subsequently added to the 3'-end by the treatment of Klenow exo-. The adaptor ligation and the PCR amplification for 18 cycles of DNA fragments were performed with Illumina (PCR primer InPE1.0 & InPE2.0).

tag: strain

tag: chip antibody

value: FLAG (SIGMA, F1804)


title: Calb2_tdTpositive_cell_33

value: RCL-tdT (Ai14)


title: Calb2_tdTpositive_cell_17

value: All

value: single cell

value: Vip Gpc3


title: Calb2_tdTpositive_cell_24

value: VISp

value: positive

value: Vip Mybpc1


title: Calb2_tdTpositive_cell_9

value: Y

value: L4 Sparcl1


title: Calb2_tdTpositive_cell_8


title: Nup98HoxA9 ES TSA-treated / anti-Crm1_ChIP

value: Crm1 (Novus Biologicals, NB100-79804)


title: Nup98HoxA9 ES LMB-treated / INPUT

value: INPUT


title: Calb2_tdTpositive_cell_7

value: L2 Ngb


title: Parental ES / anti-Crm1_ChIP

source_name: Parental ES (EB3)


title: Nup98HoxA9 ES / anti-Crm1_ChIP


title: Calb2_tdTpositive_cell_6


title: Nup98HoxA9 ES / anti-FLAG_ChIP


title: Calb2_tdTpositive_cell_4

value: Vip Chat


title: Calb2_tdTpositive_cell_5


title: Nup98HoxA9 ES TSA-treated / anti-FLAG_ChIP


title: Calb2_tdTpositive_cell_25


title: Calb2_tdTpositive_cell_2


title: Nup98HoxA9 ES / INPUT


title: Calb2_tdTpositive_cell_16


title: Nup98HoxA9 ES TSA-treated / INPUT


title: Col-0 P-_4

status: Public on Jan 03 2016

city: Beijing

first: Lichao

last: Sun

state: Beijing

address: Tsinghua University

department: Life of Science

country: China

institute: Tsinghua university

data_processing:
Remove reads contain N and adapter sequence
Remove first 12 nt of reads
Remove duplicated reads
Remove reads mapped to rRNA
Map to Arabidopsis genome using Tophat2
Calculate RPKM using DEGseq
Do the differential expression using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Expression_level_rpkm.txt contains rpkm of genes annotated in TAIR10 among 6 samples

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Col-0 P-

growth_protocol: Total RNAs were extracted from the roots of P+ and P- WT seedlings (i.e., seedling grown on P-sufficient and P-deficient media) and of P- phl2 seedlings.

extract_protocol:
The total RNAs were extracted using the RNeasy plant mini kit (Qiagen).
dUTP based strand-specific library construction protocol

treatment_protocol: Phosphate starvation

tag: developmental stage

value: seedling

tag: tissue

value: root

tag: age

value: 8 days

tag: ecotype

tag: genotype/variation

value: WT

tag: treatment

value: Phosphate deficiency


title: Calb2_tdTpositive_cell_1

tag: mouse line abbreviation

tag: driver 1

tag: reporter

value: RCL-tdT (Ai14)

tag: brain region

tag: dissection

value: All

tag: input material


title: phl2 P-_6

source_name: phl2 P-


title: Calb2_tdTpositive_cell_10

value: single cell

tag: tdtomato labelling

tag: passes qc checks

tag: primary type

tag: allen science vignette cell id


title: Col-0 P-_3


title: Parental ES / INPUT

tag: strain

tag: chip antibody


title: phl2 P-_5

tag: developmental stage

tag: tissue


title: Col-0 P+_2

source_name: Col-0 P+

tag: age

tag: ecotype

value: Phosphate sufficiency


title: Col-0 P+_1

tag: genotype/variation

tag: treatment


title: AZ_bact_only_5I

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

institute: Imperial College London

description: Small RNA

data_processing:
Adapter clipping (fastx toolkit).
Fastq to fasta (custom script in perl 5.12).
Trim to remove short reads <15 and longer than 33 (custom script perl v 5.12).
Collapse to unique reads (fastx toolkit).
Genome_build: N/A
Supplementary_files_format_and_content: Collapsed fasta files (header: >id_number of reads).

organism: Escherichia coli

source_name: OxyS-overexpressing E. coli cells, 5' independent

extract_protocol:
RNA was extracted with TRIsure according to the manufacturer's instructions.
RNA was used to generate small RNA libraries using the NEBNext small RNA kit, according to the manufacturer's instructions.

tag: strain/background

tag: cell type

value: OxyS-overexpressing bacterial cells

tag: library construction

value: 5' independent


title: Zfp42 Enhancer GFP-positive

city: Cambridge

first: Nisha

last: Rajagopal

state: Massachusetts

address: 32 Vassar Street

institute: MIT

description:
GFP-positive population after electroporation of 2 gRNAs in Zfp42 enhancer region
sample_barcode_deepseq.txt

data_processing:
Extraction of different libraries from sequenced file using known sample barcodes and primer sequence
In case of MERA, the sequenced reads were matched to the designed 3918 guide RNAs and dummy guide RNA in the bulk population,GFP-medium and negative populations.Counts for each guide RNA in each population were hence obtained based on exact matches
Genome_build: mm10
Supplementary_files_format_and_content: text files with chromosomal locations of guide RNAs and counts;

source_name: Embryonic Stem cells

growth_protocol: mESC media composed of Knockout DMEM (Life Technologies) supplemented with 15% defined fetal bovine serum (FBS) (HyClone), 0.1mM nonessential amino acids (NEAA) (Life Technologies), Glutamax (GM) (Life Technologies), 0.55mM 2-mercaptoethanol (b-ME) (Sigma), 1X ESGRO LIF (Millipore), 5 nM GSK-3 inhibitor XV and 500 nM UO126.

extract_protocol:
Life Technologies PureLink Genomic DNA mini kit
In-house designed PCR-based library preparation protocol
CRISPR/Cas9-based genomic mutation strategy followed by sequencing

tag: target gene with gfp tag

tag: gfp-type

value: GFP-replacement at TSS

tag: modifications

value: dummy guide RNA at ROSA26 locus


title: Tdgf1 URE GFP-negative

description:
GFP-neg/medium population after electroporation of 2 gRNAs in Tdgf1 URE region
sample_barcode_deepseq.txt


title: Zfp42 Enhancer GFP-negative

description:
GFP-neg/medium population after electroporation of 2 gRNAs in Zfp42 enhancer region
sample_barcode_deepseq.txt


title: Tdgf1 URE GFP-positive

description:
GFP-positive population after electroporation of 2 gRNAs in Tdgf1 URE region
sample_barcode_deepseq.txt


title: Rpp25 Bulk Replicate1

description:
Bulk population after gRNA electroporation into replicate 1 of the Rpp25-GFP line
gRNA_rpp25_counts.txt

value: C-terminal GFP-fusion


title: Nanog GFP-negative Replicate 2

description:
GFP-negative population after gRNA electroporation and FACS sorting into replicate 2 of the Nanog-GFP line
gRNA_nanog_allreps_counts.txt

value: Nanog


title: Nanog Bulk Replicate 2

description:
Bulk population after gRNA electroporation into replicate 2 of the Nanog-GFP line
gRNA_nanog_allreps_counts.txt


title: Rpp26 GFP-negative Replicate 1

description:
GFP-negative population after gRNA electroporation and FACS sorting into replicate 1 of the Rpp25-GFP line
gRNA_rpp25_counts.txt


title: Nanog GFP-negative Replicate 1

description:
GFP-negative population after gRNA electroporation and FACS sorting into replicate 1 of the Nanog-GFP line
gRNA_nanog_allreps_counts.txt


title: Tdgf1 Enhancer GFP-positive

description:
GFP-positive population after electroporation of 2 gRNAs in Tdgf1 enhancer region
sample_barcode_deepseq.txt


title: Zfp42 GFP-negative Replicate 4

description:
GFP-negative population after gRNA electroporation and FACS sorting into replicate 4 of the Zfp42-GFP line
gRNA_zfp42_allreps_counts.txt


title: Nanog Bulk Replicate1

description:
Bulk population after gRNA electroporation into replicate 1 of the Nanog-GFP line
gRNA_nanog_allreps_counts.txt


title: Zfp42 GFP-negative Replicate 3

description:
GFP-negative population after gRNA electroporation and FACS sorting into replicate 3 of the Zfp42-GFP line
gRNA_zfp42_allreps_counts.txt


title: Zfp42 GFP-medium Replicate 3

description:
GFP-medium population after gRNA electroporation and FACS sorting into replicate 3 of the Zfp42-GFP line
gRNA_zfp42_allreps_counts.txt


title: Zfp42 Bulk Replicate 3

description:
Bulk population after gRNA electroporation into replicate 3 of the Zfp42-GFP line
gRNA_zfp42_allreps_counts.txt


title: Zfp42 GFP-negative Replicate 2

description:
GFP-negative population after gRNA electroporation and FACS sorting into replicate 2 of the Zfp42-GFP line
gRNA_zfp42_allreps_counts.txt


title: Zfp42 Bulk Replicate 4

description:
Bulk population after gRNA electroporation into replicate 4 of the Zfp42-GFP line
gRNA_zfp42_allreps_counts.txt


title: Zfp42 GFP-medium Replicate 4

description:
GFP-medium population after gRNA electroporation and FACS sorting into replicate 4 of the Zfp42-GFP line
gRNA_zfp42_allreps_counts.txt


title: Zfp42 Bulk Replicate 2

description:
Bulk population after gRNA electroporation into replicate 2 of the Zfp42-GFP line
gRNA_zfp42_allreps_counts.txt


title: Tdgf1 GFP-medium Replicate 3

description:
GFP-medium population after gRNA electroporation and FACS sorting into replicate 3 of the Tdgf1-GFP line
gRNA_tdgf_allreps_counts.txt


title: Zfp42 Bulk Replicate 1

description:
Bulk population after gRNA electroporation into replicate 1 of the Zfp42-GFP line
gRNA_zfp42_allreps_counts.txt


title: Zfp42 GFP-medium Replicate 1

description:
GFP-medium population after gRNA electroporation and FACS sorting into replicate 1 of the Zfp42-GFP line
gRNA_zfp42_allreps_counts.txt


title: Tdgf1 GFP-negative Replicate 2

description:
GFP-negative population after gRNA electroporation and FACS sorting into replicate 2 of the Tdgf1-GFP line
gRNA_tdgf_allreps_counts.txt


title: Tdgf1 GFP-negative Replicate 3

description:
GFP-negative population after gRNA electroporation and FACS sorting into replicate 3 of the Tdgf1-GFP line
gRNA_tdgf_allreps_counts.txt


title: Tdgf1 Bulk Replicate 3

description:
Bulk population after gRNA electroporation into replicate 3 of the Tdgf1-GFP line
gRNA_tdgf_allreps_counts.txt


title: Zfp42 GFP-negative Replicate 1

description:
GFP-negative population after gRNA electroporation and FACS sorting into replicate 1 of the Zfp42-GFP line
gRNA_zfp42_allreps_counts.txt


title: Tdgf1 Enhancer GFP-negative

description:
GFP-neg/medium population after electroporation of 2 gRNAs in Tdgf1 enhancer region
sample_barcode_deepseq.txt


title: Tdgf1 Bulk Replicate 1

description:
Bulk population after gRNA electroporation into replicate 1 of the Tdgf1-GFP line
gRNA_tdgf_allreps_counts.txt


title: Tdgf1 GFP-medium Replicate 1

description:
GFP-medium population after gRNA electroporation and FACS sorting into replicate 1 of the Tdgf1-GFP line
gRNA_tdgf_allreps_counts.txt


title: Tdgf1 Bulk Replicate 2

description:
Bulk population after gRNA electroporation into replicate 2 of the Tdgf1-GFP line
gRNA_tdgf_allreps_counts.txt


title: STING KO 4h dAdT

city: Boston

first: Alexander

last: Poltorak

address: 150 Harrison avenue

institute: Tufts University

description:
11_S3_FPKM
Processed data file: STING-KO_unstim+23cGAMP+dAdT+DMXAAgenes.fpkm_tracking.txt

data_processing:
MiSeq Basecalls - data untrimmed - 75bp paired-end reads.
Bowtie2 2.2.4; bowtie2-align -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25
TopHat; tophat -p 4 -o
Cuffdiff 2.2.1; cuffdiff -p 4 -L
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited .txt files containing FPKM values.

source_name: peritoneal macrophages, STING KO, 4h dAdT + lipofectamine

growth_protocol: 3-5 day thioglycollate elicited macrophages seeded on tissue culture treated plates 1 day before stimulation.

extract_protocol:
Total RNA - Phenol Extraction - TriPure (Roche).
TruSeq RNA Sample Preparation Kit.

treatment_protocol: Samples treated for 4hrs by transfection with indicated agonists.

value: STING KO

value: peritoneal macrophages

tag: agonist/conditions

value: 4h dAdT + lipofectamine


title: B6.MOLF-TMEM173 congenic littermate homozygous for B6 STING DMXAA

description:
B6_Congenic_dmxaa_FPKM
B6.MOLF-Tmem(B6)
Processed data file: Congenic-dAdT+DMXAA_genes.fpkm_tracking.txt

source_name: peritoneal macrophages, B6 STING, DMXAA

value: B6 STING

value: DMXAA


title: B6.MOLF-TMEM173 congenic littermate homozygous for B6 STING 4h dAdT

description:
B6_Congenic_dAdT_FPKM
B6.MOLF-Tmem(B6)
Processed data file: Congenic-dAdT+DMXAA_genes.fpkm_tracking.txt

source_name: peritoneal macrophages, B6 STING, 4h dAdT + lipofectamine


title: STING KO 4h DMXAA

description:
12_S4_FPKM
Processed data file: STING-KO_unstim+23cGAMP+dAdT+DMXAAgenes.fpkm_tracking.txt

source_name: peritoneal macrophages, STING KO, DMXAA


title: STING KO no stimulation

description:
9_S1_FPKM
Processed data file: STING-KO_unstim+23cGAMP+dAdT+DMXAAgenes.fpkm_tracking.txt

source_name: peritoneal macrophages, STING KO, no stimulation

value: no stimulation


title: B6.MOLF-TMEM173 congenic littermate homozygous for MOLF STING 4h 2'3' cGAMP

description:
MOLF_congenic_stim_FPKM
B6.MOLF-Tmem(MOLF)
Processed data file: Congenic-unstim+23cGAMP_genes.fpkm_tracking.txt

source_name: peritoneal macrophages, MOLF STING, 4h 2'3' cGAMP + lipofectamine

value: C57BL/6 congenic

value: MOLF STING

value: 4h 2'3' cGAMP + lipofectamine


title: B6.MOLF-TMEM173 congenic littermate homozygous for B6 STING 4h 2'3' cGAMP

description:
B6_congenic_stim_FPKM
B6.MOLF-Tmem(B6)
Processed data file: Congenic-unstim+23cGAMP_genes.fpkm_tracking.txt

source_name: peritoneal macrophages, B6 STING, 4h 2'3' cGAMP + lipofectamine


title: STING KO 4h 2'3' cGAMP

description:
10_S2_FPKM
Processed data file: STING-KO_unstim+23cGAMP+dAdT+DMXAAgenes.fpkm_tracking.txt

source_name: peritoneal macrophages, STING KO, 4h 2'3' cGAMP + lipofectamine


title: B6.MOLF-TMEM173 congenic littermate homozygous for MOLF STING DMXAA

description:
MOLF_Congenic_dmxaa_FPKM
B6.MOLF-Tmem(MOLF)
Processed data file: Congenic-dAdT+DMXAA_genes.fpkm_tracking.txt

source_name: peritoneal macrophages, MOLF STING, DMXAA


title: B6.MOLF-TMEM173 congenic littermate homozygous for B6 STING no stimulation

description:
B6_congenic_FPKM
B6.MOLF-Tmem(B6)
Processed data file: Congenic-unstim+23cGAMP_genes.fpkm_tracking.txt

source_name: peritoneal macrophages, B6 STING, no stimulation


title: Zfp42 GFP-medium Replicate 2

description:
GFP-medium population after gRNA electroporation and FACS sorting into replicate 2 of the Zfp42-GFP line
gRNA_zfp42_allreps_counts.txt


title: AZ121_RDE4_5I

description: Small RNA

organism: Caenorhabditis elegans

source_name: C. elegans rde-4 fed OxyS-overexpressing E. coli, 5' independent

value: whole animal

tag: e. coli food source

value: OxyS overexpressing (AZ121)


title: GS035_N2_5I

description: Small RNA

source_name: C. elegans N2 fed OxyS-deletion mutant E. coli, 5' independent

value: OxyS deletion mutant (GS035)


title: AZ121_N2_5I

description: Small RNA

source_name: C. elegans N2 fed OxyS-overexpressing E. coli, 5' independent

value: 5' independent


title: AZ121_rde4

description: Small RNA

source_name: C. elegans rde-4 fed OxyS-overexpressing E. coli, 5' dependent

value: 5' dependent


title: HB101_N2

description: Small RNA

source_name: C. elegans N2 fed HB101 E. coli, 5' dependent


title: Fetal_liver_H3K4me3_rep1

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

institute: Liangzhu Laboratory

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to the hg19 using bwa(v0.7.5a-r405) with the default parameters. MACS (v1.4) was used for peak calling with the options “-f BED -g hs -n chip_output -B -S”.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include peak locations after MACS calling.

organism: Homo sapiens

extract_protocol:
ChIPed DNA was purified by phenol chloroform, ethanol-precipitated and was further resuspended in 10 mM Tris-HCl pH 8.0.
ChIP sequencing libraries were constructed under the standard protocol of the NEBNext® Ultra™ DNA Library Prep Kit.

value: 12 weeks after gestation

value: fetal liver

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#


title: Tdgf1 GFP-medium Replicate 2

description:
GFP-medium population after gRNA electroporation and FACS sorting into replicate 2 of the Tdgf1-GFP line
gRNA_tdgf_allreps_counts.txt

value: GFP-replacement at TSS

value: dummy guide RNA at ROSA26 locus


title: HB101_N2_5I

description: Small RNA

source_name: C. elegans N2 fed HB101 E. coli, 5' independent


title: Tdgf1 GFP-negative Replicate 1

description:
GFP-negative population after gRNA electroporation and FACS sorting into replicate 1 of the Tdgf1-GFP line
gRNA_tdgf_allreps_counts.txt

source_name: Embryonic Stem cells


title: GS035_N2

description: Small RNA

source_name: C. elegans N2 fed OxyS-deletion mutant E. coli, 5' dependent


title: Fetal_liver_H3K4me1_rep2

tag: chip antibody


title: Fetal_liver_H3K4me1_rep1

tag: developmental stage


title: Fetal_liver_H3K27me3_rep1

tag: tissue

value: CST


title: B6.MOLF-TMEM173 congenic littermate homozygous for MOLF STING no stimulation

description:
MOLF_congenic_FPKM
B6.MOLF-Tmem(MOLF)
Processed data file: Congenic-unstim+23cGAMP_genes.fpkm_tracking.txt

source_name: peritoneal macrophages, MOLF STING, no stimulation

value: peritoneal macrophages


title: B6.MOLF-TMEM173 congenic littermate homozygous for MOLF STING 4h dAdT

description:
MOLF_Congenic_dAdT_FPKM
B6.MOLF-Tmem(MOLF)
Processed data file: Congenic-dAdT+DMXAA_genes.fpkm_tracking.txt

source_name: peritoneal macrophages, MOLF STING, 4h dAdT + lipofectamine

value: 4h dAdT + lipofectamine


title: Fetal_heart_H3K4me3_rep1

value: fetal heart


title: Fetal_liver_H3K27me3_H3K4me3_Sequential_rep1

value: H3K4me3 (Abcam, ab8580)


title: Fetal_heart_H3K4me1_rep1


title: Fetal_heart_H3K4me1_rep2


title: Fetal_liver_H3K27ac_rep2

value: active motif


title: Fetal_liver_H3K27ac_rep1


title: Fetal_liver_H3K4me3_rep2


title: Input DNA

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

description: WCE Input

data_processing:
Basecalls performed using CASAVA from Illumina
ChIP-seq and Input DNA reads were aligned to the mm9 genome assembly using BOWTIE2 version 2.1.0 with the default configuration.
Aligned unique genomic location reads (sam file) transfer to bed file
The  differentially enriched/devoid (vs. TSC_B ChIP)  domains whose size are more than 500Kb or less than 5Kb are filtered out. And then, for devoided regions, defined as the intersection part from TSC specific enriched domains.
show in IGV
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files were generated from R-seg (mode 2 or mode 3).   The "scores" mean  HMM domain scores; The input DNA samples files  only contain the Bowtie alighment results.

source_name: TSC

growth_protocol: ES and TS cells are cultured with standard protocol

extract_protocol:
ChIP DNA samples were obtained with Native ChIP protocol; briefly, chromatin were fractionated and then  subject to Mnase digestion to generate mononucleosomes. Then the mononucleosome fraction was extracted with high salt buffer and H2A.X-containing nucleosomes were isolated and enriched with anti-H2A.X (Xiaolab_Maked) antibodies.
Libraries were prepared according to Illumina's standard protocol, with instructions accompanying the TruSeq ChIP DNA Sample Kit

value: TSC

tag: passage

value: passage 15 to 25

tag: strain

value: mix

tag: antibody


title: Fetal_liver_H3K27me3_H3K4me3_Sequential_rep2


title: Fetal_heart_H3K27me3_rep1


title: Fetal_heart_H3K27me3_H3K4me3_Sequential_rep2


title: AZ121_N2

description: Small RNA

source_name: C. elegans N2 fed OxyS-overexpressing E. coli, 5' dependent

value: whole animal

value: OxyS overexpressing (AZ121)


title: Fetal_heart_H3K27me3_H3K4me3_Sequential_rep1


title: iTSC_4F_5

description: ChIP

value: iTSC

value: anti-H2A.X (Xiaolab_Maked)


title: Fetal_heart_H3K27ac_rep2

value: 12 weeks after gestation


title: Fetal_heart_H3K27me3_rep2


title: Fetal_brain_H3K4me3_rep2

value: fetal brain

value: Abcam


title: Fetal_heart_H3K27ac_rep1


title: iTSC_3F_1

description: ChIP


title: Fetal_liver_H3K27me3_rep2

value: fetal liver


title: Fetal_brain_H3K4me3_rep1


title: Fetal_brain_H3K4me1_rep2


title: iTSC_3F_14

description: ChIP


title: Fetal_brain_H3K4me1_rep1


title: TSC_A

description: ChIP

source_name: TS cell


title: TSC_B

description: ChIP


title: Fetal_heart_H3K4me3_rep2


title: Fetal_brain_H3K27me3_rep2


title: ES_CTRL

description: ChIP

source_name: ES cell

value: ESC


title: Fetal_brain_H3K27ac_rep2


title: Fetal_brain_H3K27me3_rep1

value: CST


title: Fetal_brain_H3K27me3_H3K4me3_Sequential_rep1


title: Fetal_brain_H3K27me3_H3K4me3_Sequential_rep2


title: iTSC_4F_1

description: ChIP


title: Fetal_liver_RNA_seq_rep2

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to the hg19 RefSeq gft using Tophat(v2.0.9) with the default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each RefSeq genes

source_name: fetal liver

extract_protocol:
Total RNAs were extracted using the RNeasy Mini Kit (Qiagen)
RNA sequencing libraries were constructed under the standard protocol of illumina TruSeq RNA Prep Kit.

tag: age

value: 12 weeks gestation

value: fetus

value: liver


title: Fetal_liver_RNA_seq_rep1


title: Fetal_heart_RNA_seq_rep2

source_name: fetal heart

value: heart


title: Fetal_heart_RNA_seq_rep1


title: tmd8_input

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description: Input

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were trimmed to 35 nt.
Sequenced reads were mapped to human hg19 genome using BWA version 0.5.9-r16.
Non uniquely mapped reads were filtered out.
Peaks were called using  a Parzen window based algorithm (LEE et al, 2011. Nucleic Acis Res. 39(9):3558-73.)
Genome_build: hg19
Supplementary_files_format_and_content: Wig format

source_name: TMD8 ABC-DLBCL B cells

growth_protocol: The human DLBCL cell lines were grown RPMI media supplemented with 10% FBS and 2mM L-Glutamine. Media was changed every 2-3 days.

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

treatment_protocol: No additional treatment

value: Activated B Cell like Diffuse Large B Cell Lymphoma cell line

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


title: MEF

description: ChIP

source_name: MEF cells

value: MEF

value: passage 1 to 5

value: mix


title: Fetal_brain_RNA_seq_rep2

source_name: fetal brain

value: brain


title: tmd8_foxp1

description: Chromatin IP against FOXP1

value: Anti-FOXP1 polyclonal (Gift from Ed Morrisey lab)


title: Fetal_brain_RNA_seq_rep1


title: ly19_input

description: Input

source_name: OCI-Ly19 GCB-DLBCL B cells

value: Germinal Center like Diffuse Large B Cell Lymphoma cell line


title: Fetal_brain_H3K27ac_rep1

value: 12 weeks after gestation

value: fetal brain

value: active motif


title: ly10_foxp1

description: Chromatin IP against FOXP1

source_name: OCI-Ly10 ABC-DLBCL B cells


title: ly19_foxp1

description: Chromatin IP against FOXP1


title: ht_input

description: Input

source_name: HT GCG-DLBCL B cells


title: ly10_input

description: Input


title: ly8_foxp1

description: Chromatin IP against FOXP1

source_name: OCI-Ly8 GCB-DLBCL B cells


title: ly8_input

description: Input


title: ht_foxp1

description: Chromatin IP against FOXP1


title: hbl_input

description: Input

source_name: HBL-1 ABC-DLBCL B cells


title: hbl_foxp1

description: Chromatin IP against FOXP1


title: bjab_foxp1

description: Chromatin IP against FOXP1

source_name: BJAB GCB-DLBCL B cells


title: Rsp-KO 2

status: Public on Jan 02 2016

city: Bethesda

first: Michael

last: Otto

state: MD

address: 9000 Rockville Pike

department: NIAID

institute: NIH

description: processed data file:  MUTANT.Gene.rpkm.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to S. aureus USA300_FPR3757 (RefSeq accession number NC_007793.1 ) using BWA. Based on the above standard, the QC of alignment was produced.
The commonly used fragments per kilobase of transcript per million mapped fragments (RPKM) incorporate normalization steps to ensure that expression levels for different genes and transcripts can be compared across runs.
Based on RPKM normalization, we performed analyses of differentially expressed genes. Genes with an adjusted P value < 0.05, FDR < 0.001 and fold change > 2 were identified as being differentially expressed.
Genome_build: S. aureus USA300_FPR3757 (RefSeq accession number NC_007793.1; ASM1346v1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each 2 Samples

organism: Staphylococcus aureus

source_name: S. aureus

growth_protocol: Overnight cultures were diluted 1:100 into 50 ml of TSB and incubated at 37°C with shaking at 200 rpm until grown to an OD600 nm of 1.5-2.0 (mid-logarithmic growth phase).

extract_protocol:
Total RNA was isolated using an RNeasy Mini Kit (Qiagen) as recommended in a standard protocol as described before. A total of 10 μg of each RNA sample was subjected to further purification to enrich the mRNA using a MICROBExpress Kit (Ambion) according to the manufacturer's instructions.
An Illumina Paired End Sample Prep kit was used to prepare RNA-seq library according to the manufacturer's instructions.

treatment_protocol: The same bacterial CFU cultures were then collected, the cells were washed twice in 10 mM sodium phosphate buffer (pH 6.5).

value: MRSA BD02-25

tag: incubation time

value: mid-logarithmic growth phase (4h)

tag: genotype/variation

value: delta-Rsp


title: Rsp-KO 1


title: WT 1

description: processed data file:  WILD_TYPE.Gene.rpkm.txt

value: wild type


title: WT 2


title: Site 7, 11/25/2011, sediment

status: Public on Jan 01 2016

city: Charleston

first: Thomas

last: Canam

state: Illinois

address: 600 Lincoln Avenue

department: Biological Sciences

institute: Eastern Illinois University

description: 16S V4 region amplification

data_processing:
Illumina data was analyzed with Casava1.8 (pipeline 1.8).
The raw sequence output from the Illumina MiSeq v3 platform were processed using mothur v.1.20.1 (Schloss et al., 2009, Appl Environ Microbiol 75:7537-7541), where any sequences containing ambiguities or homopolymers longer than 8 bases were removed.
Chimeric and chloroplast sequences were also removed. Sequences were aligned based on comparison to the SILVA-compatible bacterial alignment database (Quast et al., 2013, Nucl Acids Res 41: D590-D596) available within mothur, and aligned sequences were trimmed to a uniform length of 250 base pairs.
After these pretreatment steps were completed, the data set included a total of 452,988 sequences for an average of 8,089 sequences per sample.
Sequences were clustered into operational taxonomic units (OTUs) based on 97% sequence identity using the nearest neighbor algorithm within mothur and exported into an Excel spreadsheet where they were sorted at the family level.

organism: riverine metagenome

source_name: sediment sample from local watershed

extract_protocol:
Total DNA was extracted from filtered (HT-200 polysulfone 0.2 µm filter membranes) samples using a FastDNA® Soil Spin Kit (MP Biomedicals). The V4 region of the 16S rRNA gene was amplified using 501-508 and 701-712 primers as previously described (Kozich et al., 2013, Appl Environ Microbiol 81:5112-5120).
The library was quantitated by qPCR and sequenced on one MiSeq Nano flowcell for 251 cycles from each end of the fragments using a MiSeq sequencing kit version 2 and analyzed with Casava1.8 (pipeline 1.8). PhiX DNA is used as a spikein control for MiSeq runs.  Most PhiX reads are removed in normal Casava processing but a few residual reads may remain. PhiX genome is 3kb in length.

tag: date

tag: media

value: benthic

tag: site


title: Site 14, 11/25/2011, sediment

description: 16S V4 region amplification


title: Site 11, 11/25/2011, sediment

description: 16S V4 region amplification


title: Site 12, 11/25/2011, sediment

description: 16S V4 region amplification


title: Site 10, 11/25/2011, sediment

description: 16S V4 region amplification


title: Site 8, 11/25/2011, sediment

description: 16S V4 region amplification


title: Site 6, 11/25/2011, sediment

description: 16S V4 region amplification


title: Site 9, 11/25/2011, sediment

description: 16S V4 region amplification


title: Site 13, 11/25/2011, sediment

description: 16S V4 region amplification


title: Site 5, 11/25/2011, sediment

description: 16S V4 region amplification


title: Site 1, 11/25/2011, sediment

description: 16S V4 region amplification


title: Site 2, 11/25/2011, sediment

description: 16S V4 region amplification


title: Site 4, 11/25/2011, sediment

description: 16S V4 region amplification


title: Site 13, 11/25/2011, water

description: 16S V4 region amplification

source_name: water sample from local watershed

value: planktonic


title: Site 10, 11/25/2011, water

description: 16S V4 region amplification


title: bjab_input

description: Input

tag: cell type


title: Site 11, 11/25/2011, water

description: 16S V4 region amplification


title: Site 9, 11/25/2011, water

description: 16S V4 region amplification


title: Site 7, 11/25/2011, water

description: 16S V4 region amplification


title: Site 8, 11/25/2011, water

description: 16S V4 region amplification


title: Site 12, 11/25/2011, water

description: 16S V4 region amplification


title: Site 6, 11/25/2011, water

description: 16S V4 region amplification


title: Site 5, 11/25/2011, water

description: 16S V4 region amplification


title: Site 4, 11/25/2011, water

description: 16S V4 region amplification


title: Site 1, 11/25/2011, water

description: 16S V4 region amplification


title: Site 3, 11/25/2011, water

description: 16S V4 region amplification


title: Site 3, 11/25/2011, sediment

description: 16S V4 region amplification


title: Site 2, 11/25/2011, water

description: 16S V4 region amplification


title: Site 14, 11/25/2011, water

description: 16S V4 region amplification


title: Site 14, 11/18/2011, sediment

description: 16S V4 region amplification


title: Site 11, 11/18/2011, sediment

description: 16S V4 region amplification


title: Sample_7P1639_KO_TA

city: Madiosn

first: Romeo

middle: S

last: Blanc

state: WI

address: 1111 Highland Ave, WIMR II, 4th floor, Blanc Lab

department: CRB

institute: University of Wisconsin-Madison

data_processing:
The raw data generated is imaged and bases are called before sequence analysis begins. Sequences generated are de-multiplexed, aligned to a reference genome and transferred to an institutional server where it is accessed by MDACC bionformaticians. Data analysis is performed in collaboration with faculty from the Department of Bioinformatics.

Genome_build: mm10
Supplementary_files_format_and_content: tar files contains raw data for each samples (separated)

source_name: PRM7 null mouse

extract_protocol:
Muscles were removed, flash frozen and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
A NGS library is made up of random fragments that represent the entire sample. It is created by shearing DNA (Covaris S220) into 150-400 bp fragments. These fragments are ligated to specific adapters. Library fragments of the appropriate size are then selected (size is application dependent) and isolated.  Following a sample cleanup step, the resultant library is quantified by qPCR and checked for quality using the Agilent Bioanalyzer. The SMF has automated library preparation for most applications using the Beckman SPRIworks system.
Cluster Generation: Library fragments are bound to a flow cell by hybridizing the fragments to a lawn of oligonucleotides complementary to the adapter sequences. Bound fragments are clonally amplified by bridge amplification to create millions of individual dense clusters of clones.  Cluster generation occurs in a closed environment on the Illumina cBOT instrument.

value: tibialis anterior (skeletal muscle)

value: 8 months


title: Sample_7P1643_KO_TA


title: Sample_7P1641_WT_TA

source_name: WT mouse


title: Sample_7P1389_WT_TA


title: Site 12, 11/18/2011, sediment

description: 16S V4 region amplification


title: Sample_7P1640_WT_TA


title: Site 8, 11/18/2011, sediment

description: 16S V4 region amplification


title: Site 9, 11/18/2011, sediment

description: 16S V4 region amplification


title: Site 7, 11/18/2011, sediment

description: 16S V4 region amplification


title: Calb2_tdTpositive_cell_13

source_name: Primary visual cortex

tag: mouse line abbreviation

tag: driver 1

tag: reporter

value: RCL-tdT (Ai14)

tag: brain region

value: VISp

tag: dissection

value: All

tag: input material

value: single cell

tag: tdtomato labelling

value: positive

tag: passes qc checks

value: Y

tag: primary type

value: Vip Chat

tag: allen science vignette cell id


title: Sample_7P1387_KO_TA

tag: tissue

tag: strain

tag: age


title: Site 5, 11/18/2011, sediment

description: 16S V4 region amplification

tag: date


title: PrdmRescue_F10R_RNAseq

city: Stanford

first: Natalie

last: Nady

state: CA

address: 265 Campus Dr.

department: Chemical and Systems Biology

institute: Stanford

data_processing:
Reads aligned to mm9 using default settings with Bowtie2.2.4
Wig files were generated with QuEST2.4
RNA-seq were aligned to mm9 and quantified against mouse ENSEMBL 78 (GRCm38) gene models using htseq-count. Variance-stabilizing transformation (VST) was applied across samples for processed data.
Genome_build: Alignments done using mm9 as reference
Supplementary_files_format_and_content: wig and tab delimited text

source_name: embryonic stem cells

growth_protocol: For maintenance all mouse ESC lines were grown in so-called “2i+LIF” medium that is serum  free N2B27-based medium supplemented with MEK inhibitor PD0325901 (0.8 μM) and GSK3β  inhibitor CHIR99021 (3.3 μM) in tissue culture (TC) dishes pretreated with 7.5 μg/ml polyL-ornithine  (Sigma) and 5 μg/ml laminine (BD) (Hayashi and Saitou, 2013; Hayashi et al., 2011). For ChIP-seq,  RNA-seq and immunoprecipitation experiments Stella:GFP mESC lines and FH-Prdm14 derivatives  were cultured for 5 days in feeder-free conditions in DMEM-high glucose medium (DMEM/high  glucose; HyClone) containing 15% (v/v) FBS, 1 mM glutamine, penicillin/streptomycin, 0.1mM  nonessential amino acids, 0.1 mM 2-mercaptoethanol and supplemented with LIF (serum+LIF  conditions).

extract_protocol:
ChIPs were performed using approximately 1-2 x 10^7 mESCs fixed with 1% formaldehyde for 10 min at room temp. RNA was extracted using Trizol.
Sequencing libraries were prepared starting from ~30ng of ChIP DNA or oligo-dT purified mRNA using the NEBNext Multiplex Oligos for Illumina kit (Cat# E7335S).

tag: genotype

value: Prdm14-/- + FLAG-HA-Prdm14


title: Site 6, 11/18/2011, sediment

description: 16S V4 region amplification

tag: media

tag: site


title: Site 4, 11/18/2011, sediment

description: 16S V4 region amplification


title: Mtgr1null_C3_RNAseq


title: Site 3, 11/18/2011, sediment

description: 16S V4 region amplification


title: PrdmRescue_G6R_RNAseq


title: Site 2, 11/18/2011, sediment

description: 16S V4 region amplification


title: Prdm14null_G6_RNAseq


title: Site 1, 11/18/2011, sediment

description: 16S V4 region amplification


title: Site 13, 11/18/2011, sediment

description: 16S V4 region amplification


title: Site 10, 11/18/2011, sediment

description: 16S V4 region amplification


title: E14_H32_K27_AcK_R1

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
reads were aligned to mm10 using TopHat v2.0.9 and Bowtie v2.1.0
differential gene expression analysis was performed using cufflinks/cuffdiff v2.2.0
Data was analyzed and visualized using R and CummeRbund
Genome_build: mm10

source_name: Embryonic stem cell E14

growth_protocol: ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.

extract_protocol:
Total RNA was extracted using Qiagen RNEasy Mini Kit Protocol
Library construction and sequencing was performed by Bejing Genomics Institute (http://www.genomics.cn/en/index) The total RNA samples are first treated with DNase I. Then the mRNA is enriched by using the oligo(dT) magnetic beads (for  eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then the first strand of cDNA is  synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End  reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the  QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library.

treatment_protocol: Unnatural amino acid was added as a stock solution in ddH2O or weighed in and directly dissolved in 1x culture medium

tag: cell line

tag: transgene 1

tag: transgene 2

value: H3.2 K27TAG/4xPylT

tag: unnatural amino acid

value: 24h 10 mM AcK


title: E14_H32_K27_AcK_R2


title: Site 10, 11/18/2011, water

description: 16S V4 region amplification


title: Site 12, 11/18/2011, water

description: 16S V4 region amplification


title: E14_H33_K64_AcK_R2

value: H3.3 K64TAG/4xPylT


title: Site 8, 11/18/2011, water

description: 16S V4 region amplification


title: E14_H33_K37_AcK_R2

value: H3.3 K37TAG/4xPylT


title: E14_H33_K56_AcK_R2

value: H3.3 K56TAG/4xPylT


title: E14_H33_K64_AcK_R1


title: E14_H33_K56_AcK_R1


title: E14_H33_K37_AcK_R1


title: Prdm14null_F10_RNAseq


title: E14_H33_K27_AcK_R2

value: H3.3 K27TAG/4xPylT


title: E14_H33_K27_AcK_R1


title: Site 5, 11/18/2011, water

description: 16S V4 region amplification

value: planktonic


title: Site 6, 11/18/2011, water

description: 16S V4 region amplification


title: Site 7, 11/18/2011, water

description: 16S V4 region amplification


title: Site 4, 11/18/2011, water

description: 16S V4 region amplification


title: E14_H33_K23_AcK_R2

value: H3.3 K23TAG/4xPylT


title: E14_H33_K23_AcK_R1


title: wt2_2i_RNAseq

value: wild type


title: E14_H33_K9_AcK_R2

value: H3.3 K9TAG/4xPylT


title: Site 2, 11/18/2011, water

description: 16S V4 region amplification


title: Site 13, 11/18/2011, water

description: 16S V4 region amplification


title: Site 14, 11/18/2011, water

description: 16S V4 region amplification


title: E14_H33_K9_AcK_R1


title: Site 1, 11/18/2011, water

description: 16S V4 region amplification


title: Site 9, 11/18/2011, water

description: 16S V4 region amplification


title: E14_H33_AcK_R2


title: E14_H33_AcK_R1


title: E14_H33_ctrl_R2

value: 24h no UAA


title: E14_AcKRS_AcK_R1


title: E14_AcKRS_AcK_R2


title: E14_H33_ctrl_R1


title: No_NusA_2

city: University Park

first: Paul

last: Babitzke

state: PA

address: 203 Althouse Laboratory

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

data_processing:
Quality trimming of the dataset was performed using trimmomatic. Reads containg 'oligo' were extracted and oligos were removed using '--discard-untrimmed' option of cutadapt.
Both whole data set and oligo read data set were aligned separately to Bacillus subtilis subsp. subtilis str. 168 reference genome using BWA short read aligner.
genome coverage graphs were generated using bedtools and visualized using IGV.
Terminators were identified as thelocal maxima of average coverage from the oligo-mapping.
Terminator efficency were calculated using the average mapped reads upstream and downstream of terminator point.
Genome_build: gi|255767013|ref|NC_000964.3| Bacillus subtilis subsp. subtilis str. 168
Supplementary_files_format_and_content: bedgraph files where column4 has the read-coverage from the whole dataset and oligo dataset corresponding to the reference genomic position. Tab-delimited text files containing no.of reads mapped to each gene, their differential expression fold change and details of terminators identified.

organism: Bacillus subtilis

source_name: Exponential phase cells

growth_protocol: Minimal-ACH medium (Spizizen salts, 0.2% acid-hydrolyzed casein, 0.5% glucose) supplemented with 12.5 μg/ml tetracycline ± 30 μM IPTG

extract_protocol:
RNA was isolated from frozen pellets using the RNeasy kit (Qiagen), residual DNA was removed by DNase treatment.
Total RNA was dephosphorylated (CIP) and treated with Ribo-Zero™ kit for rRNA removal. A small RNA-oligo was ligated to 3’ end of the RNA and illumina libraries were generated using TruSeq® stranded mRNA library kit.

value: NusA-depletion strain (PLBS802)

tag: growth condition

value: Exponential (100 Klett)

tag: inducer

value: No IPTG


title: No_NusA_5


title: No_NusA_6


title: No_NusA_4


title: No_NusA_3


title: E14_AcK_R1


title: E14_ctrl_R2


title: E14_AcK_R2


title: No_NusA_1


title: Plus_NusA_6

value: 30 μM IPTG


title: Plus_NusA_3


title: Plus_NusA_5


title: Plus_NusA_4


title: E14_cl2_CPK_R2

value: 48h 0.2 mM CpK


title: E14_ctrl_R1


title: Site 11, 11/18/2011, water

description: 16S V4 region amplification


title: E14_cl2_CPK_R1


title: Site 3, 11/18/2011, water

description: 16S V4 region amplification


title: Plus_NusA_2


title: Plus_NusA_1


title: E14_cl2_ctrl_R2

value: 48h no UAA


title: E14_cl1_CPK_R2


title: E14_cl2_ctrl_R1


title: E14_cl1_CPK_R1


title: E14_cl1_ctrl_R2


title: E14_cl1_ctrl_R1


title: 3T3_cl2_CPK_R2

source_name: Embryonic Fibroblast 3T3


title: 3T3_cl1_CPK_R2


title: 3T3_cl2_ctrl_R1


title: 3T3_cl2_ctrl_R2


title: 3T3_cl1_ctrl_R1


title: meristems; sterile plants; growing; b3_sterile

city: Zurich

first: Samuel

middle: Elias

last: Wuest

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description: RNA-seq meristems growing sterile plants

data_processing:
Sequencing reads were mapped against the Arabidopsis genome (TAIR v10) using the subread software and default parameter (Liao et al., 2013), and sorted and indexed using the samtools software (Li et al., 2009).
Reads were assigned to genes using the featureCounts-function implemented in the R package Rsubread (Liao et al., 2014) and gene definitions from TAIR version 10 (www.arabidopsis.org).
Normalization factors for count data from different libraries were calculated using the weighted trimmed mean of M-values (Robinson and Oshlack, 2010).
Genome_build: TAIR v10
Supplementary_files_format_and_content: matrix of scaled counts per gene per million reads

source_name: shoot apical meristematic regions

growth_protocol: Plants of Arabidopsis thaliana accessions Landsberg erecta (L-er), ap3-1 (NASC-Code N3085, see www.arabidopsis.info) and male sterile 1 (ms1-1, NASC-Code N75) were grown on soil (ED73, Universalerde, Germany) covered with a thin quartz sand layer, in a growth chamber at the Institute of Evolutionary Biology and Environmental Studies under 16 hours light (at 20°C and 5 kLux) and 8 hours dark (at 16°C) and 60% humidity. The positions of individual plants were fully randomized, and regularly changed (at least every 10 days).

extract_protocol:
Total RNA was extracted using the PicoPure RNA isolation kit (Life Technologies), including the DNAseI-treatment as recommended in the technical manual. Two to four caps containing tissue sections were pooled on-column. For each RNA-Seq replicate, between 16 and 31 embedded inflorescences were sectioned and mounted onto slides, which resulted in 58 to 91 laser-dissected meristem sections that were pooled per replicate.
For RNA-Seq, RNA was amplified using the NuGEN Ovation 3’DGE amplification kit, according to the technical manual.

treatment_protocol: For laser-assisted microdissection (LAM) inflorescences from at least 20 individual plants were collected on ice and fixed in Ethanol:Acetic Acid 3:1 [v/v] under vacuum (~ 500 mBar) for 2x10 min at 4°C and then left in the fixative overnight at 4°C. The tissue was embedded into Paraplast X-tra Embedding Media (Sigma-Aldrich) using an automated protocol and the Leica ASP200 embedding machine as follows: 1h 70% EtOH, 3x1h 90% EtOH, 3x 1h 100% EtOH, 2x 1h 100% Xylol, 1x 15 min. 100% Xylol, all at room temperature, and then 2x 1h Paraplast X-tra and 1x 3h Paraplast X-tra at 56 °C. Inflorescences were then poured into paraplast blocks and cooled at 4°C until use. Embedded samples were sectioned on a Leica RM2145 microtome to 10 μm thickness and mounted on membrane-slides (Molecular Machines and Industries (MMI), Glattbrugg, Switzerland) using sterile water for mounting. The slides were then dried overnight at 42°C on a heating table and laser-dissected immediately. LAM was performed on an MMI CellCut Plus after dewaxing the tissue sections for 2x 10 minutes in Xylol, and several meristematic regions were pooled on a single collection cap.

value: laser-dissected shoot apex (meristematic region)

value: ms1-1 homozygous

tag: reproductive status

value: sterile

tag: growth status

value: growing


title: 3T3_cl1_CPK_R1


title: meristems; fertile plants; fruits removed; b3_reactiv

department: Institute of Evolutionary Biology and Environmental Studies

description: RNA-seq re-activated meristems fertile plants after fruit removal

value: ms1-1 co-segregant

value: fertile; fruits removed (48 hrs prior to tissue collection)

value: arrested; fruits removed


title: PBS_sample12

city: Philadelphia

first: Ali

middle: B

last: Rodgers

address: 380 S. University Ave, 476 Hill Pavilion

department: Biomedical Sciences

institute: University of Pennsylvania, School of Veterinary Medicine

description: PBS injected at zygote stage

data_processing:
Align reads to ribosomal sequences and repeats to remove from downstream analysis
Process sequences through the RUM pipeline according to Grant et. al (2011) Comparative analysis of RNA-Seq alignment algorithms and  the RNA-Seq unified mapper (RUM). Bioinformatics 27(18):2518–2528.
Differential expression with EdgeR using the EDGE package
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file containing RPKM values for each aligned sequence (ROWS) by each biological sample (COLUMN)

source_name: PVN

growth_protocol: 12h light dark cycles, food ad libitum, weaned at postnatal day 28 into same-sex group housing

extract_protocol:
Whole brains were collected from 18-20wk male mice anesthetized with isoflurane and preserved at -80C. PVN tissue for each animal was micropunched from two successive 300 µm brain slices (-0.50 to -0.80 and -0.80 to -1.10 relative to bregma) using a hollow 1.0 mm needle (Ted Pella). Tissue was treated TRIzol reagent (Invitrogen) and bath sonicated on ice with 30 s on/off cycles for 2.5 min (brain). Total brain RNA was isolated by miRNeasy kit (Qiagen).
Illumina single-end cDNA libraries of adult male PVN mRNA were prepared from 250 ng total RNA using the TruSeq Stranded mRNA Kit with poly-A enrichment (RS-122-2101) according to manufacturer’s protocol.

treatment_protocol: C57/Bl6:129S6/SvEvTac hybrid mouse zygotes microinjected with of 9 miRs together (1 ng/uL final concentration of 0.11 ng/uL each miRIDIAN mimic miR-29c, miR-30a, miR-30c, miR-32, miR-193-5p, miR-204, miR-375, miR-532-3p, miR-698 in 1X DPBS) or to 1X DPBS only. Zygotes were subsequently implanted into surrogate CD1 dams and reared normally.

tag: Sex

value: male

value: brain


title: meristems; sterile plants; growing; b2_sterile


title: meristems; sterile plants; arrested; b3_arrested2

description: RNA-seq meristems arrested fertile plants

value: fertile

value: arrested


title: PBS_sample9

description: PBS injected at zygote stage


title: meristems; fertile plants; fruits removed; b2_reactiv


title: meristems; fertile plants; arrested; b2_arrested2


title: meristems; fertile plants; growing; b3_growing

description: RNA-seq meristems growing fertile plants


title: PBS_sample8

description: PBS injected at zygote stage


title: 3T3_cl1_ctrl_R2


title: meristems; fertile plants; growing; b1_Ler_growing

value: Ler wild type


title: PBS_sample10

description: PBS injected at zygote stage


title: PBS_sample11

description: PBS injected at zygote stage


title: meristems; fertile plants; arrested; b1_Ler_arrested


title: meristems; sterile plants; growing; b1_ap3_sterile

value: Ler; ap3-1


title: miR_sample5

description: miR injected at zygote stage


title: PBS_sample7

description: PBS injected at zygote stage


title: miR_sample4

description: miR injected at zygote stage


title: miR_sample6

description: miR injected at zygote stage


title: miR_sample3

description: miR injected at zygote stage


title: 3T3_cl2_CPK_R1


title: miR_sample2

description: miR injected at zygote stage


title: meristems; fertile plants; growing; b2_growing2


title: miR_sample1

description: miR injected at zygote stage


title: mESC

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

data_processing:
illumina Casava software used for basecalling
mESC, mNPC and mMN reads were mapped to mm9 whole genome and transcriptome using tophat with parameters -a 4 -m 0 --min-intron-length 10 --max-intron-length 1000000 --initial-read-mismatches 4 --min-isoform-fraction 0.0 --num-threads 3 --max-multihits 5 --solexa1.3-quals --library-type fr-firststrand --segment-mismatches 2
Exon inclusion ratios were calculated using a splicetrap program
Genome_build: mm9
Supplementary_files_format_and_content: Text files include exon inclusion level values for each sample.

source_name: mouse embryonic stem cell (mESC)

growth_protocol: 46C mESCs were cultured on gelatin, in mESC media supplemented with LIF. mNPCs were cultured on poly-ornithine and fibronectin coated plates, in mNPC media supplemented with EGF and FGF. mMNs were derived in the presence of RA and SAG, and isolated with FACS.

extract_protocol:
Total RNA was collected with the Trizol reagent. Poly-A RNA was selected for using oligo-dT beads.
Libraries were constructed with the Illumina TruSeq stranded kit. A final library of 300-400 bp was size selection with an agarose gel.
The libraries were subjected to 100bp paired-end sequencing (Illumina HiSeq2000).

tag: cell type

value: mESC


title: mNPC

source_name: mouse neuronal progenitor cell (mNPC)

tag: protocol

value: mESCs were differentiated into mNPCs


title: meristems; fertile plants; fruits removed; b1_Ler_reactiv

tag: tissue


title: mESC PTBP1 iCLIP

data_processing:
PCR duplicates were removed by comparing random portions of the sequenced barcodes. Unique reads were mapped to the mouse genome (mm9/NCBI37) using Bowtie, allowing up to two nucleotide mismatches. Mapped reads were further mapped to the Known Gene table .
iClip data analyses were performed following the published paper (Konig J*, Zarnack K*, Curk T, Gregor R, Kayikci M, Zupan,B, Luscombe NM, Ule J (2010))
Genome_build: mm9
Supplementary_files_format_and_content: bed files (*_PTBP1 FDR <0.01, clustered within 20nt neighborhood and at least contained 4 significant reads) include exon inclusion level values for each sample.

growth_protocol: 46C mESCs were cultured on gelatin, in mESC media supplemented with LIF. 46C mNPCs were cultured on poly-ornithine and fibronectin coated plates, in mNPC media supplemented with EGF and FGF.

extract_protocol:
Total RNA was collected following the iCLIP protocol.
Libraries were constructed using the ICLIP protocol.
The libraries were subjected to 100bp single-end sequencing (Illumina HiSeq2000).

treatment_protocol: 46C mESCs and mNPCs were cross-linked at 100 mJ/cm2.

value: ESC

tag: antibody

value: rabbit anti-PTBP1 antibody (PTB-NT) described in PMID:11003644


title: mESC PTBP1-PTBP2 siRNA #2

description:
PTBP1 and PTBP2 siRNA knockdown #2
mESC_PTBP1-2kd_splicetrap.txt

data_processing:
Sequenced reads were mapped to mm9 genome using TopHat.
Exon inclusion ratios were calculated using SpliceTrap.
Genome_build: mm9
Supplementary_files_format_and_content: Text files include exon inclusion level values for each sample.

growth_protocol: 46C mESCs were cultured on gelatin, in mESC media supplemented with LIF.

extract_protocol:
Total RNA was collected with the Trizol reagent. Poly-A RNA was selected for using oligo-dT beads.
Libraries were constructed with the Illumina TruSeq stranded kit. A final library of 300-400 bp was size selection with an agarose gel.
The libraries were subjected to 50bp paired-end sequencing (Illumina HiSeq2000).

treatment_protocol: mESCs were reverse transfected with 20 nM of either control, PTBP1, or PTBP1-PTBP2 siRNA. After 24 hours, the mESCs were supplemented with an addition 20 nM of siRNA.

value: 46C mESC

tag: treatment

value: siPtbp1 #2 & siPtbp2 #2


title: mESC Control siRNA #1 rep B

description:
Transfection siRNA Control #1 biological replicate B
mESC_Control_splicetrap.txt

value: siControl #1


title: mESC PTBP1-PTBP2 siRNA #1 rep B

description:
PTBP1 and PTBP2 siRNA knockdown #1 biological replicate B
mESC_PTBP1-2kd_splicetrap.txt

value: siPtbp1 #1 & siPtbp2 #1


title: mESC Control siRNA #1 rep A

description:
Transfection siRNA Control #1 biological replicate A
mESC_Control_splicetrap.txt


title: mESC PTBP1-PTBP2 siRNA #1 rep A

description:
PTBP1 and PTBP2 siRNA knockdown #1 biological replicate A
mESC_PTBP1-2kd_splicetrap.txt


title: mESC PTBP1 siRNA #2

description:
PTBP1 siRNA knockdown #2
mESC_PTBP1kd_splicetrap.txt

value: siPtbp1 #2


title: mESC PTBP1 siRNA #1 rep B

description:
PTBP1 siRNA knockdown #1 biological replicate B
mESC_PTBP1kd_splicetrap.txt

value: siPtbp1 #1


title: mESC PTBP1 siRNA #1 rep A

description:
PTBP1 siRNA knockdown #1 biological replicate A
mESC_PTBP1kd_splicetrap.txt


title: GFP+ mMN

source_name: GFP+ mouse motor neuron (mMN)

value: mESCs were differentiated into mMNs


title: mESC siRNA Control siRNA #2

description:
Transfection siRNA Control #2
mESC_Control_splicetrap.txt

value: siControl #2


title: mNPC PTBP1-PTBP2 siRNA #2

description:
PTBP1 and PTBP2 siRNA knockdown #2
mNPC_PTBP1-2kd_splicetrap.txt

data_processing:
illumina Casava software used for basecalling
Exon inclusion ratios were calculated using a splicetrap program
Genome_build: mm9
Supplementary_files_format_and_content: Text files include exon inclusion level values for each sample.

growth_protocol: 46C mNPCs were cultured on poly-ornithine and fibronectin coated plates, in mNPC media supplemented with EGF and FGF.

treatment_protocol: mNPCs were reverse transfected with 10 nM of either control, Ptbp1, Ptbp2, or Ptbp1-Ptbp2 siRNA. After 48 hours, the mNPCs were harvested for total RNA.


title: mNPC Control siRNA #1

description:
Transfection siRNA Control #1
mNPC_Control_splicetrap.txt


title: mNPC PTBP1 iCLIP

value: NPC


title: mNPC PTBP1 siRNA #2

description:
PTBP1 siRNA knockdown #2
mNPC_PTBP1kd_splicetrap.txt


title: mNPC PTBP1-PTBP2 siRNA #1

description:
PTBP1 and PTBP2 siRNA knockdown #1
mNPC_PTBP1-2kd_splicetrap.txt


title: mNPC PTBP2 siRNA #1

description:
PTBP2 siRNA knockdown #1
mNPC_PTBP2kd_splicetrap.txt

value: siPtbp2 #1


title: mNPC PTBP1 siRNA #1

description:
PTBP1 siRNA knockdown #1
mNPC_PTBP1kd_splicetrap.txt


title: D2 MN Pbx1 I6 +/- clone #5

data_processing:
Sequenced reads were mapped to mm9 genome using TopHat. FPKM values were calculated using the Cufflinks package.
Genome_build: mm9
Supplementary_files_format_and_content: Text files include exon inclusion level values for each sample.

source_name: Day 2 mouse motor neuron cultures (D2 MN)

growth_protocol: HB9 mESCs were grown in aggregate culture in the presence of RA and SAG.

extract_protocol:
Total RNA was collected with the Trizol reagent. Poly-A RNA was selected for using oligo-dT beads.
Libraries were constructed with the Illumina TruSeq stranded kit.
The libraries were subjected to 50bp single-end sequencing (Illumina HiSeq2000).

treatment_protocol: I6 +/- clones were treated with transiently transfected with Cas9 and guide RNA sequences to generate heterozygous deletions at the Pbx1 intron 6 locus.

value: HB9-GFP mESC

tag: genotype/variation

value: Pbx1 I6 +/- CRISPR deletion

value: mESC clones were harvested after Day 2 of differentiation in MN media


title: D2 MN Pbx1 I6 +/- clone #3


title: D2 MN Pbx1 I6 +/- clone #2


title: D2 MN Pbx1 I6 +/- clone #4


title: mNPC Control siRNA #2

description:
Transfection siRNA Control #2
mNPC_Control_splicetrap.txt


title: D2 MN clone #3

value: Wildtype Control


title: D2 MN clone #1


title: MtgrRescue_C1R_RNAseq

tag: strain

tag: genotype

value: Mtgr1-/- + FLAG-HA-Mtgr1


title: MtgrRescue_C3R_RNAseq


title: mNPC PTBP2 siRNA #2

description:
PTBP2 siRNA knockdown #2
mNPC_PTBP2kd_splicetrap.txt

value: mESCs were differentiated into mNPCs

value: siPtbp2 #2


title: RNA-seq: Adar10

first: Allissa

middle: A

last: Dillman

address: Center for Cancer Research National Cancer Institute Building 41, Room B626

department: Center for Cancer Research

institute: NCI

data_processing:
Tophat (v2.0.6)/Bowtie (2.02.0)
HT-SEQ
DESeq
DEXSeq
Samtools mpileup (samtools-01.19.0)
Genome_build: mm9
Supplementary_files_format_and_content: CSV DESEQ and DEXSEQ output, and A-to-I edit sites

source_name: Frontal Cortex

extract_protocol:
Trizol
TruSeq stranded total RNA sample preparation kit, ribo-Zero gold rRNA removal beads

value: Adar2+/+ Gria2R/R

tag: gender

value: male


title: Mtgr1null_C1_RNAseq


title: Mtgr1null_A3_RNAseq


title: MutantRescue_E294K_F10_RNAseq

value: Prdm14-/- + FLAG-HA-Prdm14 E294K mutant


title: RNA-seq: Adar7


title: RNA-seq: Adar11


title: RNA-seq: Adar6


title: wt_serum_RNAseq

value: wild type


title: RNA-seq: Adar12


title: MutantRescue_E294K_G6_RNAseq


title: RNA-seq: Adar4


title: RNA-seq: Adar9


title: input DNA_ChIPseq


title: RNA-seq: Adar3


title: RNA-seq: Adar1


title: wt_HA_ChIPseq


title: D2 MN Pbx1 I6 +/- clone #1


title: PrdmRescue_G6R_HA_ChIPseq

value: Prdm14-/- + FLAG-HA-Prdm14