title: Drosophila willistoni female body small RNA [M045_dwil_female_body]

city: Stanford

first: Jaaved

last: Mohammed

address: 265 Campus Drive

department: Chemical and Systems Biology

institute: Stanford University

description: female bodies

data_processing:
3' adapter sequences were trimmmed using the fastx_clipper utility
reads < 15nt in size were filtered
identical read sequences were collapsed using the fastq_collapser utility
Supplementary_files_format_and_content: read count table files (columns are read read sequence and number of reads)

organism: Drosophila willistoni

source_name: D. willistoni female body small RNA

extract_protocol:
Male and female bodies were isolated in bulk using sieves after sorting by sex. Animals were flash frozen in liquid nitrogen followed by vortexing. This procedure severs heads from the thorax and abdomen allowing separation of these two body parts when sifted through chilled fine mesh sieves. Here we used a .600mm sieve to collect male bodies. Total RNA was then extracted from the bodies using TRIzol according to manufacturer protocol.
For Illumina GAII Libraries: From total RNA, ~18-26 nt fraction was isolated using PAGE and cloned using ligation to adapters requiring 5' monophosphate and 3' OH.
For Illumina HiSeq Library: Libraries were created with the Illumina truseq small RNA cloning kit using a modified protocol. Small RNAs in the 18-29nt size range were first isolated from total RNA by PAGE purification before cloning. PAGE purification was also performed after ligation of RNAs to 3’ and 5’ linkers before processing in subsequent steps. All enzymatic reactions and oligos were used as indicated by manufacturer.

value: abdomen and thorax


title: L2L3-24

status: Public on Nov 20 2017

type: SRA

city: La Jolla

first: Carsten

last: Pfeffer

state: CA

address: 9500 Gilman Drive

country: USA

institute: UCSD

description:
CP-H_64
L2-L3_tpm5.txt

library_source: transcriptomic

data_processing:
Illumina Casava 1.8 for basecalling
Reads were demultiplexed, trimmed, and filtered (prinseq, parameters: -lc_method dust –lc_threshold 15 –trim_left 7) before mapping (bowtie2, standard parameters; (Langmead and
Salzberg, 2012)) the reads to the mouse transcriptome (ENSEMBLE cDNA sequences or ab initio predicted genes), the ERCC transcriptome and mapped reads counted (htseq-count;
(Anders et al., 2014)) following the Cel-seq general pipeline.
Genome_build: Ensemble cDNA sequences or ab initio predicted genes; mouse ensemble release v76; GRCm38.p2
Supplementary_files_format_and_content: tab-delimited text files include tpm values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: cortex

extract_protocol:
Mice aged P35 or older were anaesthetized with ketamine and xylazine (100mg*kg-1 and 10mg*kg-1, respectively), perfused transcardially with cold sucrose solution (in mM: NaCl, 83;
KCl, 2.5; MgSO4, 3.3; NaH2PO4, 1; NaHCO3, 26.2; D-glucose, 22; sucrose, 72; and CaCl2, 0.5, bubbled with 95% O2 and 5% CO2) and decapitated, and the visual cortex was cut into
300µm coronal or tangential sections in cold sucrose solution. Slices were incubated in sucrose solution in a submerged chamber at 34°C for 30min and then at room temperature (21°C) until
used for RNA harvest from patch-clamped cells.
RNA was harvested as described previously (Pfeffer et al., 2013). In brief, slices were mounted under a 40x 0.8 NA water lens and superfused with sucrose solution (same as in slice
preparation). Cells were identified using GFP or tdTomato  fluorescence and visualized with IR-DIC. Cells were then patched with regular RNAse free patch pipettes (2-4 MOhm resistance) in
whole-cell mode using the voltage-clamp configuration. After seal establishment and break-in the cell was held at -70mV and the cell content including cell nucleus was harvested using
negative pressure and expelled in an Eppendorf tube and frozen at -70C. Intracellular solution was RNAse free: in mM: CsMeSO4, 115; NaCl, 4; HEPES, 10; Na3GTP, 0.3; MgATP, 4; EGTA,
0.3; BAPTA(4Cs), 10; adjusted to pH 7.4 with CsOH; mOsm 295. The procedures lasted approximately 2-3 minutes per cell (from targeting to tube freezing).
Single cell RNA-seq was carried out following the Cel-seq protocol (Hashimshony et al., 2016; Hashimshony et al., 2012). RT and second strand synthesis were performed using Superscript
III (Invitrogen) and second strand synthesis kit (Invitrogen), respectively, before IVT amplification (Maxiscript T7, Ambion). 96 samples (up to 94 cells and 2-8 control samples) were
handled in parallel to construct one sequencing library. After library fragmentation (Mg-Acetat + heat) and 3’ adaptor attachment, 11-15 cycles of PCR were used for library amplification (final
concentration > 1ng/microL, library peak fragment size ~350 nt). Libraries were sequenced using Illumina HiSeq 2500 and HiSeq 4000 at the UCSD genomics core (1st read 13 cycles for
the barcode, 2nd read 50 cycles for the 3’ end of the transcript).

tag: strain

value: 129S2/SvPasCrl, CD-1 mix

tag: age

value: postnatal day >p35

tag: genotype

value: SepW1-Cre, WT

tag: position

value: visual cortex layer 2


title: V1AL-2

description:
CP-N_10
V1ALPr-V1PMPr_tpm5.txt

value: primary visual cortex layer 2

tag: axonal projection

value: visual ctx layer 2 -> anterior lateral


title: L2L3-27

description:
CP-H_67
L2-L3_tpm5.txt


title: Spt4 AA mutant 15min 0.4M NaCl 30ºC rep3

city: Barcelona

first: Francesc

last: Posas

address: Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

description:
replicate 3
57_17750_CAGATC

data_processing:
Raw sequencing reads were mapped to the sacCer3 genome using TopHat2 v2.1.0
Quantification was performed with featureCounts v1.5.1 using the Ensembl R64-1-1 annotation.
Differential expression testing was performed using DESeq2 v1.14.1
Genome_build: sacCer3
Supplementary_files_format_and_content: DESeq2_raw_counts.tsv contains raw read counts obtained via featureCounts after alignment. Each column represents one sample in lexicographical order.

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: Wild-type and Spt4-AA mutant strains were grown to log-phase on YPD medium at 30ºC (no stress) and then subjected to osmotic stress (15 min 0.4M NaCl).

extract_protocol:
Total RNA was extracted with standard hot-phenol protocol.
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 (ref. RS-122-2101) according to the manufacturer's protocol starting with 1 µg of total RNA for poly(A)-mRNA selection. Libraries were analyzed with the Agilent Bioanalyzer using a DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to sequencing with 50 bp single-end reads on Illumina's HiSeq 2500 with v4 sequencing chemistry.

treatment_protocol: Untreated (no stress) / osmotic stress (15 min 0.4M NaCl)

value: BY4741 (MATa his3-delta 1 leu2-delta 0 met15-delta 0 ura3-delta 0) SPT4(T42A/S43A)-TAP::kanMX4


title: L5Front-45

description:
CP-T_80
L5Cal-L5Front_tpm5.txt

value: visual cortex layer 5

value: layer 5 -> frontal ctx


title: L2L3-26

description:
CP-H_66
L2-L3_tpm5.txt


title: L2L3-25

description:
CP-H_65
L2-L3_tpm5.txt


title: L3L2-22

description:
CP-H_63
L2-L3_tpm5.txt

value: visual cortex layer 3


title: Spt4 AA mutant 15min 0.4M NaCl 30ºC rep1

description:
replicate 1
55_17899_GAGTGG


title: L5Front-46

description:
CP-T_81
L5Cal-L5Front_tpm5.txt


title: L5Cal-28

description:
CP-T_8
L5Cal-L5Front_tpm5.txt

value: layer 5 -> contralateral ctx


title: L5Front-43

description:
CP-T_78
L5Cal-L5Front_tpm5.txt


title: L3L2-27

description:
CP-H_73
L2-L3_tpm5.txt


title: Drosophila willistoni head small RNA [M020_dwil_head]

description: heads

source_name: D. willistoni head small RNA

tag: tissue

value: head


title: Spt4 WT 15min 0.4M NaCl 30ºC rep3

description:
replicate 3
51_17744_ACAGTG

value: BY4741 (MATa his3-delta 1 leu2-delta 0 met15-delta 0 ura3-delta 0) SPT4-TAP::kanMX4


title: L3L2-21

description:
CP-H_62
L2-L3_tpm5.txt


title: L5Front-42

description:
CP-T_77
L5Cal-L5Front_tpm5.txt


title: Spt4 AA mutant 15min 0.4M NaCl 30ºC rep2

description:
replicate 2
56_17900_GATCAG


title: Spt4 AA mutant no stress rep3

description:
replicate 3
54_17747_GCCAAT


title: L5Front-40

description:
CP-T_75
L5Cal-L5Front_tpm5.txt


title: Spt4 AA mutant no stress rep2

description:
replicate 2
53_17746_CGATGT


title: L5Front-41

description:
CP-T_76
L5Cal-L5Front_tpm5.txt


title: L3L2-19

description:
CP-H_60
L2-L3_tpm5.txt


title: L3L2-20

description:
CP-H_61
L2-L3_tpm5.txt


title: Spt4 AA mutant no stress rep1

description:
replicate 1
52_17745_CGTACG


title: L3L2-18

description:
CP-H_59
L2-L3_tpm5.txt


title: Spt4 WT 15min 0.4M NaCl 30ºC rep2

description:
replicate 2
50_17743_TTAGGC


title: L2L3-23

description:
CP-H_58
L2-L3_tpm5.txt


title: Spt4 WT no stress rep3

description:
replicate 3
48_17741_TGACCA


title: Spt4 WT 15min 0.4M NaCl 30ºC rep1

description:
replicate 1
49_17742_GTCCGC


title: Spt4 WT no stress rep1

description:
replicate 1
46_17739_CCGTCC


title: Spt4 WT no stress rep2

description:
replicate 2
47_17740_CGTACG


title: L2L3-21

description:
CP-H_56
L2-L3_tpm5.txt


title: L2L3-22

description:
CP-H_57
L2-L3_tpm5.txt


title: L5Front-37

description:
CP-T_72
L5Cal-L5Front_tpm5.txt


title: L5Front-36

description:
CP-T_71
L5Cal-L5Front_tpm5.txt


title: L5Front-39

description:
CP-T_74
L5Cal-L5Front_tpm5.txt


title: Drosophila erecta embryo small RNA [M057_dere_embryo]

description: mixed embryos

organism: Drosophila erecta

source_name: D. erecta embryo small RNA

value: whole embryo


title: Drosophila erecta female body small RNA [M055_dere_female_body]

description: female bodies

source_name: D. erecta female body small RNA


title: L2L3-19

description:
CP-H_54
L2-L3_tpm5.txt


title: Drosophila sechellia female body small RNA [M054_dsec_female_body]

description: female bodies

organism: Drosophila sechellia

source_name: D. sechellia female body small RNA


title: Drosophila yakuba head small RNA [V058_dyak_head]

description: heads

organism: Drosophila yakuba

source_name: D. yakuba head small RNA


title: L2L3-20

description:
CP-H_55
L2-L3_tpm5.txt


title: L5Cal-27

description:
CP-T_7
L5Cal-L5Front_tpm5.txt


title: L5Front-35

description:
CP-T_70
L5Cal-L5Front_tpm5.txt


title: Drosophila yakuba head small RNA [V052_dyak_head]

description: heads


title: Drosophila yakuba embryo small RNA [V046_dyak_embryo]

description: mixed embryos

source_name: D. yakuba embryo small RNA


title: L3L2-17

description:
CP-G_53
L2-L3_tpm5.txt


title: L5Front-34

description:
CP-T_69
L5Cal-L5Front_tpm5.txt


title: Drosophila mojavensis head small RNA [V056_dmoj_head]

description: heads

organism: Drosophila mojavensis

source_name: D. mojavensis head small RNA


title: L5Front-33

description:
CP-T_68
L5Cal-L5Front_tpm5.txt


title: Drosophila mojavensis head small RNA [V049_dmoj_head]

description: heads


title: L3L2-16

description:
CP-G_52
L2-L3_tpm5.txt


title: Drosophila mojavensis male body small RNA [V110_dmoj_male_body]

description: male bodies

source_name: D. mojavensis male body small RNA


title: Drosophila virilis embryo small RNA [V047_dvir_embryo]

description: mixed embryos

organism: Drosophila virilis

source_name: D. virilis embryo small RNA


title: L5Front-32

description:
CP-T_67
L5Cal-L5Front_tpm5.txt


title: Drosophila mojavensis embryo small RNA [V041_dmoj_embryo]

description: mixed embryos

source_name: D. mojavensis embryo small RNA


title: L3L2-15

description:
CP-G_51
L2-L3_tpm5.txt


title: L3L2-14

description:
CP-G_50
L2-L3_tpm5.txt


title: L5Front-31

description:
CP-T_66
L5Cal-L5Front_tpm5.txt


title: Drosophila virilis head small RNA [V053_dvir_head]

description: heads

source_name: D. virilis head small RNA


title: Drosophila virilis male body small RNA [V116_dvir_male_body]

description: male bodies

source_name: D. virilis male body small RNA


title: L3L2-13

description:
CP-G_49
L2-L3_tpm5.txt


title: Drosophila yakuba female body small RNA [M043_dyak_female_body]

description: female bodies

source_name: D. yakuba female body small RNA


title: Drosophila yakuba head small RNA [M026_dyak_head]

description: heads


title: L2L3-17

description:
CP-G_47
L2-L3_tpm5.txt


title: L2L3-18

description:
CP-G_48
L2-L3_tpm5.txt


title: L5Front-29

description:
CP-T_64
L5Cal-L5Front_tpm5.txt


title: MEF_G9aKO_Hesp_Input

city: Montreal

first: Carol

last: Chen

state: QC

address: 1001 Decarie Boulevard, Rm E01.4380

department: Human Genetics

country: Canada

institute: Research Institute of McGill University Hospital Centre

library_source: genomic

data_processing:
BAM file: Sequence reads were mapped to mm9 using BWA (Li & Durbin, 2009) using default parameters. File includes unique and multiple aligned reads.
BigWig: Reads having identical coordinates were collapsed into a single read and reads with mapQ >=5 passed to FindPeaks 3.1 (Fejes et al 2008) for visualization.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: MEFs

growth_protocol: ESCs were grown in DMEM supplemented with 15% FBS (HyClone), 20 mM Hepes, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol, 100 U/mL penicillin, 0.05 mM streptomycin, leukemia inhibitory factor (1000 U/ml), and 2 mM glutamine on gelatinized plates. MEFs were grown in DMEM supplemented with 10% FBS (HyClone), 100 U/mL penicillin, 0.05 mM streptomycin, and 2 mM glutamine.

extract_protocol:
For crosslinked MNase ChIP, cells were crosslinked (1% formaldehyde, 10mins) and digested with microccocal nuclease, nuclei were then isolated and flash frozen. For native ChIP, flash frozen cell pellets were lysed with hypotonic buffer and digested with micrococcal nuclease. Protein:DNA complexes were immunoprecipitated with specific antibodies pre-bound to protein A/G or goat anti-mouse IgG magnetic beads. Eluted DNA underwent crosslink reversal, if necessary, were RNAse treated followed by phenol:choloroform cleanup.    Cells harvested and flash frozen using liquid nitrogen. RNA was then extracted using Sigma GenElute Mammalian Total RNA Extraction Kit RNA-seq libraries were prepared from mRNA as described in Morin et al from 10ug of DnaseI treated total RNA (Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, McDonald H, Varhol R, Jones S, Marra M: Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques 2008, 45:81-94.)
Adaptor ligation based library construction for paired-end Illumina sequencing

tag: cell type

value: embryonic fibroblasts

tag: Sex

value: female

tag: treatment

value: 200nM Hesperadin, 3h

tag: chip protocol

tag: chip antibody


title: L5Front-30

description:
CP-T_65
L5Cal-L5Front_tpm5.txt

value: 129S2/SvPasCrl, CD-1 mix


title: L5Front-28

description:
CP-T_63
L5Cal-L5Front_tpm5.txt

value: postnatal day >p35


title: MEF_G9aKO_Hesp_H3S10ph

value: Crosslinked MNAse


title: MEF_G9aFF_Hesp_Input_H3S10ph

value: WT


title: MEF_G9aKO_Input


title: L2L3-16

description:
CP-G_46
L2-L3_tpm5.txt

value: SepW1-Cre, WT

value: visual cortex layer 2


title: MEF_G9aKO_H3K9me2

value: Native

value: H3K9me2 (Abcam ab1220)


title: L5Front-27

description:
CP-T_62
L5Cal-L5Front_tpm5.txt

value: visual cortex layer 5

value: layer 5 -> frontal ctx


title: L2L3-15

description:
CP-G_45
L2-L3_tpm5.txt


title: L2L3-14

description:
CP-G_44
L2-L3_tpm5.txt


title: L5Front-26

description:
CP-T_61
L5Cal-L5Front_tpm5.txt


title: MEF_Hesp_Input

value: 129 X OLA


title: Drosophila yakuba embryo small RNA [M056_dyak_embryo]

description: mixed embryos


title: MEF_G9aFF_Input


title: L5Front-25

description:
CP-T_60
L5Cal-L5Front_tpm5.txt


title: 30 ' following contextual fear conditioning rep4 (FC9)

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

description:
Sono-seq
FC9

data_processing:
Library strategy: Sono-Seq
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to mm9 whole genome using Bowtie 2.
To avoid artifacts from clonal PCR amplification, identical reads (3 or more reads of the same sequence) were removed if they were present in isolation. Reads were filtered for mapping quality and removed if the likelyhood of mapping to the bext match location was less than 50%.
To analyze differential enrichment of Sono-seq signal between fear conditioned (FC) and home-cage controls (HC) we developed a novel bioinformatics strategy using the R statistical language we named “DEScan” (Supplementary Figure 1). Parameters: min_bin 50bp max_win 20, Zthersh 30, carriers 4.
DEscan is optimized to perform best on epigenetic HTS data that is not defined by genomic sequence and produces broad peaks. DEScan code and user manual are provided through the article associated with this submission.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file contains location of peaks reproducible in 4 samples Z score >30 used to assemble the cont matrix. Count matrix provided as supplementary file

growth_protocol: C57BL/6J adult male mice (2 months of age) were obtained from Jackson Laboratories and housed individually for a week on a 12 hr. /12 hr. light/dark schedule with lights on at 7 am (Zeitgeber time (ZT) 0). Food and water were available ad libitum throughout the experiment.

extract_protocol:
Thirty minutes after fear conditioning, mice were sacrificed and the hippocampus was rapidly dissected. The hippocampus was finely chopped and placed into 500 µl 2% PFA for 10 minutes to crosslink tissue. Crosslinking was stopped by the addition of 100 µl 1M glycine, tissue was washed 3x in ice cold PBS containing protease inhibitor cocktail (Sigma-Aldrich St. Louis, MO), and frozen at -80°C. Chromatin was prepared by dounce homogenizing the tissue in 1 mL ChIP cell lysis buffer (10 mM Tris HCl pH 8.1, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40), centrifuging at 5500g for 5 minutes at 4°C, removing the supernatant, and resuspending the pellet in 300 µl ChIP nuclear lysis buffer (50 mM Tris pH 8.1, 5 mM EDTA, 1% SDS). Chromatin was sonicated using a Bioruptor sonicator with the following conditions: 30 sec on, 1 min off for 15 minutes, add ice and cool sonicator, 30 sec on, 1 min off for 100 another 15 minutes. Chromatin was centrifuged for 5 minutes at 14000g at 4C and the supernatant was removed. Chromatin size was tested by removing an aliquot, reversing crosslinks, cleaning DNA using the Qiagen MinElute PCR purification kit (Qiagen Valencia, CA), quantification by NanoDrop (Thermo Scientific Whatham, MA), and running the DNA on a 1% agarose gel. Sono-seq DNA was prepared by removing 1 µg sonicated chromatin. The next morning, 4 µl 0.5M EDTA, 8 µl 1M Tris-HCl pH 7.5, and 1 µl Proteinase K (Roche Diagnostics) were added and samples were incubated an additional hour at 65°C. Samples were purified into 30 µl using the Qiagen MinElute PCR purification kit.
Library preparation for Sono-seq was performed using a combination of the ChIP-seq DNA sample prep kit and the Multiplexing Sample Preparation Oligonucleotide Kit (Illumina San Diego, CA). End repair and adenylation was performed as described by the ChIP protocol, while adapter ligation was performed as described by the Multiplexing protocol. A gel slice 300bp +/1 25bp was cut from the gel for size selection, the Qiagen Gel Extraction kit was used to purify DNA and 23 PCR cycles were used following the PCR reactions described by the Multiplexing kit. The final product was run on a gel and purified into 15µl by the Qiagen Gel Extraction kit again. Sequencing Libraries were quantified using the KAPA Library Quantification kit, normalized to 10 nM, and submitted to the PGFI sequencing core at the University of Pennsylvania for 100bp single-end sequencing on an Illumina HiSeq2000 resulting in an average of 148 million reads per sample.

treatment_protocol: Each animal was handled daily for 3 days prior to contextual fear conditioning (FC). Handling consisted of manipulation of the animals for 1-2 minutes per mouse in the same room as the experimental setting without exposure to the context. The conditioning protocol entailed a single 2-second, 1.5-mA foot shock, terminating at 2.5 minutes after placement of the mouse in the chamber, starting at 10 am (ZT3) daily. Tissue was collected at 30 minutes after FC (FC). Testing was performed at 24 hours after training over a 5-minute interval, which is sufficient to induce reconsolidation [27, 28]. The average freezing was 55 +/- 10%. Tissue was immersed in RNAlater (Qiagen) and immediately frozen. Animals that were handled but not trained were dissected at the same time of day (CC).

value: hippocampus

value: 2 months old

value: male

tag: stress

value: contextual fear conditioning


title: L3L2-12

description:
CP-G_43
L2-L3_tpm5.txt

value: visual cortex layer 3


title: L5Cal-26

description:
CP-T_6
L5Cal-L5Front_tpm5.txt

value: layer 5 -> contralateral ctx


title: L3L2-11

description:
CP-G_42
L2-L3_tpm5.txt

value: 129S2/SvPasCrl, CD-1 mix


title: 30 ' following contextual fear conditioning rep3 (FC6)

description:
Sono-seq
FC6


title: 30 ' following contextual fear conditioning rep2 (FC4)

description:
Sono-seq
FC4


title: L5Front-24

description:
CP-T_59
L5Cal-L5Front_tpm5.txt

value: postnatal day >p35


title: L3L2-10

description:
CP-G_41
L2-L3_tpm5.txt


title: control rep3 (HC6)

description:
Sono-seq
HC6

source_name: control

value: control


title: control rep4 (HC9)

description:
Sono-seq
HC9


title: control rep2 (HC4)

description:
Sono-seq
HC4


title: L5Front-23

description:
CP-T_58
L5Cal-L5Front_tpm5.txt

source_name: cortex


title: L3L2-9

description:
CP-G_40
L2-L3_tpm5.txt


title: MEF_G9aFF_Hesp_H3S10ph

value: embryonic fibroblasts

value: WT

value: female

value: 200nM Hesperadin, 3h

value: Crosslinked MNAse


title: control rep1  (HC1)

description:
Sono-seq
HC1


title: MEF_G9aFF_H3K9me2

value: Native

value: H3K9me2 (Abcam ab1220)


title: L2L3-13

description:
CP-G_38
L2-L3_tpm5.txt

value: SepW1-Cre, WT

value: visual cortex layer 2


title: L5Front-21

description:
CP-T_56
L5Cal-L5Front_tpm5.txt

value: visual cortex layer 5

value: layer 5 -> frontal ctx


title: MEF_Ctrl_H3S10ph

value: 129 X OLA

value: DMSO vehicle treated


title: MEF_Ctrl_Input


title: MEF_Hesp_H3S10ph


title: L5Front-20

description:
CP-T_55
L5Cal-L5Front_tpm5.txt


title: ESC_G9aKO_H3K36me3

source_name: 2-3 ESCs

value: embryonic stem cell

value: male

value: H3K36me3 (Abcam ab9050)


title: L2L3-11

description:
CP-G_36
L2-L3_tpm5.txt

value: 129S2/SvPasCrl, CD-1 mix

value: postnatal day >p35


title: L5Front-19

description:
CP-T_54
L5Cal-L5Front_tpm5.txt


title: 30 ' following contextual fear conditioning rep1 (FC1)

description:
Sono-seq
FC1

value: hippocampus

value: 2 months old

value: contextual fear conditioning


title: ESC_G9aKO_H3K4me3

value: H3K4me3 (Abcam ab1012)


title: L2L3-10

description:
CP-G_35
L2-L3_tpm5.txt


title: ESC_GlpKO_ssRNAseq

molecule: polyA RNA

source_name: Cd12 ESCs

value: Glp-/-


title: ESC_GlpKO_H3K4me3

value: Native


title: L5Front-38

description:
CP-T_73
L5Cal-L5Front_tpm5.txt

value: SepW1-Cre, WT


title: L2L3-9

description:
CP-G_34
L2-L3_tpm5.txt

value: visual cortex layer 2


title: ESC_GlpKO_H3K36me3


title: L5Front-18

description:
CP-T_53
L5Cal-L5Front_tpm5.txt

value: visual cortex layer 5


title: ESC_TT2_H3K4me3

source_name: TT2 ESCs

value: WT


title: L5Front-17

description:
CP-T_52
L5Cal-L5Front_tpm5.txt

value: layer 5 -> frontal ctx


title: L2L3-8

description:
CP-G_33
L2-L3_tpm5.txt


title: L5Front-16

description:
CP-T_51
L5Cal-L5Front_tpm5.txt


title: L5Front-22

description:
CP-T_57
L5Cal-L5Front_tpm5.txt


title: ESC_GlpKO_Hesp_Input

value: 200nM Hesperadin, 3h

value: Crosslinked MNAse


title: L2L3-7

description:
CP-G_32
L2-L3_tpm5.txt


title: ESC_GlpKO_Hesp_H3S10ph

value: embryonic stem cell

value: male


title: L5Front-15

description:
CP-T_50
L5Cal-L5Front_tpm5.txt

value: 129S2/SvPasCrl, CD-1 mix


title: L2L3-12

description:
CP-G_37
L2-L3_tpm5.txt

value: postnatal day >p35


title: ESC_G9aKO_ssRNAseq


title: ESC_H3.3S10A.2_H3K9me2

value: H3K9me2 (Abcam ab1220)


title: ESC_H3.3S10A.1_H3K9me2


title: ESC_GlpKO_H3K9me2


title: L5Front-14

description:
CP-T_49
L5Cal-L5Front_tpm5.txt


title: L3L2-7

description:
CP-G_28
L2-L3_tpm5.txt

value: visual cortex layer 3


title: L3L2-8

description:
CP-G_29
L2-L3_tpm5.txt


title: L2L3-6

description:
CP-G_31
L2-L3_tpm5.txt


title: ESC_H3.3S10A.2_YFP

value: GFP (Abcam ab290)


title: L5Front-13

description:
CP-T_48
L5Cal-L5Front_tpm5.txt


title: ESC_TT2_ssRNAseq


title: L5Cal-25

description:
CP-T_5
L5Cal-L5Front_tpm5.txt

value: layer 5 -> contralateral ctx


title: L3L2-6

description:
CP-G_27
L2-L3_tpm5.txt


title: L5Front-12

description:
CP-T_47
L5Cal-L5Front_tpm5.txt


title: ESC_TT2_H3K36me3

value: H3K36me3 (Abcam ab9050)


title: ESC_TT2_H3K9me2

value: Native


title: L3L2-5

description:
CP-G_26
L2-L3_tpm5.txt

value: SepW1-Cre, WT


title: L5Front-11

description:
CP-T_46
L5Cal-L5Front_tpm5.txt


title: ESC_TT2_Hesp_H3S10ph


title: ESC_TT2_Ctrl_Input

value: DMSO vehicle treated


title: ESC_TT2_Input


title: L5Front-10

description:
CP-T_45
L5Cal-L5Front_tpm5.txt

value: visual cortex layer 5


title: ESC_TT2_H3S10ph

value: WT


title: L3L2-4

description:
CP-G_25
L2-L3_tpm5.txt


title: ESC_Fucci_SG2M_Input

value: FUCCI S/G2/M-sorted


title: ESC_H3.3WT_H3K9me2

value: H3.3YFP+ C3


title: L5Front-9

description:
CP-T_43
L5Cal-L5Front_tpm5.txt

value: layer 5 -> frontal ctx


title: ESC_H3.3S10A.1_YFP

value: embryonic stem cell


title: L5Front-7

description:
CP-T_41
L5Cal-L5Front_tpm5.txt


title: ESC_H3.3WT_YFP

value: male


title: ESC_Fucci_S_H3S10ph

value: FUCCI S-sorted

value: Crosslinked MNAse


title: L3L2-2

description:
CP-G_23
L2-L3_tpm5.txt

value: 129S2/SvPasCrl, CD-1 mix

value: postnatal day >p35


title: ESC_Fucci_SG2M_H3S10ph


title: ESC_Fucci_S_Input


title: L5Front-8

description:
CP-T_42
L5Cal-L5Front_tpm5.txt


title: L3L2-1

description:
CP-G_22
L2-L3_tpm5.txt

value: visual cortex layer 3


title: L5Front-6

description:
CP-T_40
L5Cal-L5Front_tpm5.txt


title: ESC_TT2_Hesp_Input

value: 200nM Hesperadin, 3h


title: L2L3-5

description:
CP-G_21
L2-L3_tpm5.txt

value: visual cortex layer 2


title: L2L3-4

description:
CP-G_20
L2-L3_tpm5.txt


title: 10-week epithelial cell 63

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Reads were aligned to the mouse genome using Subread version 1.4.6
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's built-in NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: mammary gland

extract_protocol:
Freshly sorted basal and luminal epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis.
Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 using standard Illumina protocols.

value: FVB/NJ

tag: time stage

value: Adult

tag: cell source

value: Total epithelium


title: L2L3-3

description:
CP-G_19
L2-L3_tpm5.txt

value: SepW1-Cre, WT


title: L3L2-3

description:
CP-G_24
L2-L3_tpm5.txt


title: 10-week epithelial cell 61


title: L2L3-2

description:
CP-G_18
L2-L3_tpm5.txt


title: L5Front-5

description:
CP-T_38
L5Cal-L5Front_tpm5.txt

value: visual cortex layer 5


title: L5Front-4

description:
CP-T_36
L5Cal-L5Front_tpm5.txt


title: 10-week epithelial cell 59


title: 10-week epithelial cell 58


title: 10-week epithelial cell 60


title: L2L3-1

description:
CP-G_17
L2-L3_tpm5.txt


title: 10-week epithelial cell 62


title: 10-week epithelial cell 66


title: 10-week epithelial cell 57


title: L6L2-17

description:
CP-D_6
L2-L6_tpm5.txt

value: visual cortex layer 6


title: ESC_Fucci_G1_H3S10ph

value: WT

value: FUCCI G1-sorted


title: L5Front-3

description:
CP-T_34
L5Cal-L5Front_tpm5.txt

value: layer 5 -> frontal ctx


title: 10-week epithelial cell 65


title: L5Front-2

description:
CP-T_33
L5Cal-L5Front_tpm5.txt


title: 10-week epithelial cell 64


title: 10-week epithelial cell 56


title: L5Front-1

description:
CP-T_32
L5Cal-L5Front_tpm5.txt


title: L5Cal-24

description:
CP-T_4
L5Cal-L5Front_tpm5.txt

value: layer 5 -> contralateral ctx


title: 10-week epithelial cell 54


title: 10-week epithelial cell 53


title: 10-week epithelial cell 52


title: 10-week epithelial cell 55


title: L6L2-15

description:
CP-D_4
L2-L6_tpm5.txt


title: 10-week epithelial cell 51


title: L5Cal-23

description:
CP-T_31
L5Cal-L5Front_tpm5.txt


title: L6L2-14

description:
CP-D_3
L2-L6_tpm5.txt


title: L5Cal-22

description:
CP-T_30
L5Cal-L5Front_tpm5.txt


title: 10-week epithelial cell 49


title: 10-week epithelial cell 48


title: L6L2-13

description:
CP-D_1
L2-L6_tpm5.txt


title: 10-week epithelial cell 46


title: L5Cal-21

description:
CP-T_3
L5Cal-L5Front_tpm5.txt


title: L5Cal-20

description:
CP-T_29
L5Cal-L5Front_tpm5.txt


title: L2L6-17

description:
CP-C_93
L2-L6_tpm5.txt


title: L2L6-16

description:
CP-C_92
L2-L6_tpm5.txt


title: 10-week epithelial cell 44


title: L6L2-16

description:
CP-D_5
L2-L6_tpm5.txt


title: 10-week epithelial cell 47


title: L5Cal-18

description:
CP-T_27
L5Cal-L5Front_tpm5.txt


title: 10-week epithelial cell 43


title: L5Cal-19

description:
CP-T_28
L5Cal-L5Front_tpm5.txt


title: L2L6-14

description:
CP-C_90
L2-L6_tpm5.txt


title: 10-week epithelial cell 45


title: 10-week epithelial cell 41


title: 10-week epithelial cell 42


title: L2L6-13

description:
CP-C_89
L2-L6_tpm5.txt


title: 10-week epithelial cell 50


title: 10-week epithelial cell 40


title: 10-week epithelial cell 38


title: L5Cal-17

description:
CP-T_24
L5Cal-L5Front_tpm5.txt


title: 10-week epithelial cell 37


title: 10-week epithelial cell 39


title: L2L6-12

description:
CP-C_88
L2-L6_tpm5.txt


title: 10-week epithelial cell 36


title: L2L6-15

description:
CP-C_91
L2-L6_tpm5.txt


title: L5Cal-15

description:
CP-T_22
L5Cal-L5Front_tpm5.txt


title: 10-week epithelial cell 35


title: ESC_Fucci_G1_Input

value: embryonic stem cell

value: male


title: 10-week epithelial cell 33


title: L2L6-11

description:
CP-C_87
L2-L6_tpm5.txt

value: 129S2/SvPasCrl, CD-1 mix


title: L5Cal-14

description:
CP-T_21
L5Cal-L5Front_tpm5.txt

value: postnatal day >p35


title: L2L6-10

description:
CP-C_86
L2-L6_tpm5.txt


title: 10-week epithelial cell 34


title: 10-week epithelial cell 32


title: L5Cal-13

description:
CP-T_20
L5Cal-L5Front_tpm5.txt


title: 10-week epithelial cell 31


title: L5Cal-12

description:
CP-T_2
L5Cal-L5Front_tpm5.txt


title: L2L6-9

description:
CP-C_85
L2-L6_tpm5.txt


title: L2L6-8

description:
CP-C_84
L2-L6_tpm5.txt


title: 10-week epithelial cell 29


title: L5Cal-16

description:
CP-T_23
L5Cal-L5Front_tpm5.txt


title: 10-week epithelial cell 28


title: L6L2-11

description:
CP-C_82
L2-L6_tpm5.txt


title: L5Cal-10

description:
CP-T_18
L5Cal-L5Front_tpm5.txt


title: L5Cal-11

description:
CP-T_19
L5Cal-L5Front_tpm5.txt


title: L5Cal-9

description:
CP-T_17
L5Cal-L5Front_tpm5.txt


title: 10-week epithelial cell 25


title: 10-week epithelial cell 30


title: 10-week epithelial cell 22


title: 10-week epithelial cell 24


title: 10-week epithelial cell 23


title: 10-week epithelial cell 26


title: 10-week epithelial cell 27


title: L5Cal-8

description:
CP-T_16
L5Cal-L5Front_tpm5.txt


title: L6L2-12

description:
CP-C_83
L2-L6_tpm5.txt


title: 10-week epithelial cell 21


title: L5Cal-7

description:
CP-T_15
L5Cal-L5Front_tpm5.txt


title: 10-week epithelial cell 20


title: 10-week epithelial cell 19


title: L6L2-10

description:
CP-C_81
L2-L6_tpm5.txt


title: 10-week epithelial cell 17


title: 10-week epithelial cell 18


title: L6L2-8

description:
CP-C_79
L2-L6_tpm5.txt


title: L6L2-9

description:
CP-C_80
L2-L6_tpm5.txt


title: L5Cal-5

description:
CP-T_13
L5Cal-L5Front_tpm5.txt


title: L6L2-7

description:
CP-C_78
L2-L6_tpm5.txt


title: 10-week epithelial cell 15


title: L5Cal-4

description:
CP-T_12
L5Cal-L5Front_tpm5.txt


title: 10-week epithelial cell 14


title: L6L2-6

description:
CP-C_77
L2-L6_tpm5.txt


title: 10-week epithelial cell 16


title: 10-week epithelial cell 13


title: 10-week epithelial cell 12


title: L5Cal-3

description:
CP-T_11
L5Cal-L5Front_tpm5.txt


title: L6L2-5

description:
CP-C_76
L2-L6_tpm5.txt


title: 10-week epithelial cell 11


title: L5Cal-2

description:
CP-T_10
L5Cal-L5Front_tpm5.txt


title: L5Cal-1

description:
CP-T_1
L5Cal-L5Front_tpm5.txt


title: 10-week epithelial cell 8


title: L2L6-7

description:
CP-C_74
L2-L6_tpm5.txt


title: L2L6-6

description:
CP-C_73
L2-L6_tpm5.txt


title: L2L6-5

description:
CP-C_72
L2-L6_tpm5.txt


title: L6Cal-53

description:
CP-R_90
L6Cal-L6Thal_tpm5.txt

value: layer 6 -> contralateral ctx


title: 10-week epithelial cell 9


title: L5Cal-6

description:
CP-T_14
L5Cal-L5Front_tpm5.txt


title: 10-week epithelial cell 6


title: 10-week epithelial cell 5


title: 10-week epithelial cell 4


title: 10-week epithelial cell 3


title: L6Cal-52

description:
CP-R_9
L6Cal-L6Thal_tpm5.txt


title: L6L2-4

description:
CP-C_69
L2-L6_tpm5.txt


title: L2L6-4

description:
CP-C_71
L2-L6_tpm5.txt


title: L6Cal-51

description:
CP-R_89
L6Cal-L6Thal_tpm5.txt


title: 10-week epithelial cell 2


title: 10-week epithelial cell 1


title: 4.7 - 4.9 week epithelial cell 135

value: Puberty


title: L6Cal-50

description:
CP-R_88
L6Cal-L6Thal_tpm5.txt


title: 10-week epithelial cell 10


title: 4.7 - 4.9 week epithelial cell 134


title: L6L2-3

description:
CP-C_68
L2-L6_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 133


title: L6L2-2

description:
CP-C_67
L2-L6_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 136


title: 10-week epithelial cell 7


title: L6L2-1

description:
CP-C_66
L2-L6_tpm5.txt


title: L6Cal-49

description:
CP-R_87
L6Cal-L6Thal_tpm5.txt


title: L6Cal-48

description:
CP-R_86
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 131


title: 4.7 - 4.9 week epithelial cell 132


title: 4.7 - 4.9 week epithelial cell 130


title: L6Cal-47

description:
CP-R_85
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 129


title: 4.7 - 4.9 week epithelial cell 128


title: L6Cal-46

description:
CP-R_84
L6Cal-L6Thal_tpm5.txt


title: L2L6-2

description:
CP-C_63
L2-L6_tpm5.txt

value: visual cortex layer 2


title: L2L6-1

description:
CP-C_61
L2-L6_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 126

value: FVB/NJ


title: 4.7 - 4.9 week epithelial cell 127


title: VIP-43

description:
CP-D_9
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt

value: c57bl6, CD-1 mix

value: postnatal day >p21

value: VIP-Cre x Rosa-tdTomato

value: visual cortex layer 2/3


title: 4.7 - 4.9 week epithelial cell 125

value: Total epithelium


title: 4.7 - 4.9 week epithelial cell 124


title: L6Cal-44

description:
CP-R_82
L6Cal-L6Thal_tpm5.txt

value: SepW1-Cre, WT

value: visual cortex layer 6


title: 4.7 - 4.9 week epithelial cell 123


title: SOM-60

description:
CP-D_82
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt

value: SOM-Cre x Rosa-tdTomato


title: 4.7 - 4.9 week epithelial cell 121


title: SOM-59

description:
CP-D_81
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: SOM-58

description:
CP-D_80
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 118


title: L6Cal-41

description:
CP-R_8
L6Cal-L6Thal_tpm5.txt


title: L6Cal-42

description:
CP-R_80
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 120


title: L2L6-3

description:
CP-C_64
L2-L6_tpm5.txt


title: L6Cal-43

description:
CP-R_81
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 122


title: 4.7 - 4.9 week epithelial cell 117


title: 4.7 - 4.9 week epithelial cell 119


title: L6Thal-32

description:
CP-R_78
L6Cal-L6Thal_tpm5.txt

value: layer 6 -> thalamus


title: L6Cal-40

description:
CP-R_76
L6Cal-L6Thal_tpm5.txt


title: VIP-42

description:
CP-D_8
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 113


title: L6Cal-45

description:
CP-R_83
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 115


title: SOM-57

description:
CP-D_79
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 114


title: SOM-56

description:
CP-D_78
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: L6Cal-39

description:
CP-R_75
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 111


title: 4.7 - 4.9 week epithelial cell 112


title: 4.7 - 4.9 week epithelial cell 110


title: L6Cal-38

description:
CP-R_74
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 109


title: SOM-54

description:
CP-D_76
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 116


title: L6Cal-37

description:
CP-R_73
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 108


title: 4.7 - 4.9 week epithelial cell 104


title: L6Cal-36

description:
CP-R_72
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 107


title: 4.7 - 4.9 week epithelial cell 106


title: 4.7 - 4.9 week epithelial cell 105


title: SOM-52

description:
CP-D_73
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: SOM-53

description:
CP-D_75
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: SOM-51

description:
CP-D_72
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: L6Cal-35

description:
CP-R_71
L6Cal-L6Thal_tpm5.txt


title: L6Cal-34

description:
CP-R_70
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 103


title: 4.7 - 4.9 week epithelial cell 102


title: 4.7 - 4.9 week epithelial cell 101


title: L6Cal-33

description:
CP-R_7
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 99


title: 4.7 - 4.9 week epithelial cell 100


title: SOM-49

description:
CP-D_70
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: SOM-50

description:
CP-D_71
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 98


title: SOM-55

description:
CP-D_77
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: SOM-48

description:
CP-D_69
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 96


title: L6Cal-31

description:
CP-R_68
L6Cal-L6Thal_tpm5.txt


title: L6Cal-32

description:
CP-R_69
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 97


title: 4.7 - 4.9 week epithelial cell 95


title: SOM-47

description:
CP-D_68
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 94


title: 4.7 - 4.9 week epithelial cell 93


title: L6Cal-30

description:
CP-R_67
L6Cal-L6Thal_tpm5.txt


title: L6Cal-29

description:
CP-R_66
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 92


title: 4.7 - 4.9 week epithelial cell 91


title: SOM-46

description:
CP-D_67
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 90


title: 4.7 - 4.9 week epithelial cell 89


title: L6Cal-28

description:
CP-R_65
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 88


title: SOM-44

description:
CP-D_65
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 87


title: L6Cal-26

description:
CP-R_63
L6Cal-L6Thal_tpm5.txt


title: SOM-43

description:
CP-D_64
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 85


title: 4.7 - 4.9 week epithelial cell 86


title: 4.7 - 4.9 week epithelial cell 84


title: L6Thal-31

description:
CP-R_62
L6Cal-L6Thal_tpm5.txt


title: SOM-42

description:
CP-D_63
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 83


title: SOM-41

description:
CP-D_62
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: L6Thal-30

description:
CP-R_61
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 82


title: 4.7 - 4.9 week epithelial cell 81


title: 4.7 - 4.9 week epithelial cell 80


title: L6Thal-29

description:
CP-R_60
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 79


title: SOM-45

description:
CP-D_66
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 78


title: L6Cal-25

description:
CP-R_6
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 77


title: L6Cal-27

description:
CP-R_64
L6Cal-L6Thal_tpm5.txt


title: SOM-38

description:
CP-D_59
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: L6Thal-28

description:
CP-R_59
L6Cal-L6Thal_tpm5.txt


title: SOM-37

description:
CP-D_58
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 76


title: 4.7 - 4.9 week epithelial cell 75


title: 4.7 - 4.9 week epithelial cell 73


title: SOM-36

description:
CP-D_57
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 72


title: L6Thal-26

description:
CP-R_56
L6Cal-L6Thal_tpm5.txt


title: SOM-35

description:
CP-D_56
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 71


title: L6Thal-25

description:
CP-R_55
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 70


title: SOM-40

description:
CP-D_61
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 69


title: L6Thal-24

description:
CP-R_54
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 67


title: SOM-39

description:
CP-D_60
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: SOM-33

description:
CP-D_54
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 66


title: L6Cal-24

description:
CP-R_53
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 65


title: SOM-32

description:
CP-D_53
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 64


title: 4.7 - 4.9 week epithelial cell 63


title: 4.7 - 4.9 week epithelial cell 74


title: 4.7 - 4.9 week epithelial cell 62


title: L6Thal-27

description:
CP-R_57
L6Cal-L6Thal_tpm5.txt


title: L6Cal-23

description:
CP-R_52
L6Cal-L6Thal_tpm5.txt


title: SOM-30

description:
CP-D_51
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 61


title: 4.7 - 4.9 week epithelial cell 60


title: L6Cal-21

description:
CP-R_50
L6Cal-L6Thal_tpm5.txt


title: SOM-29

description:
CP-D_50
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 58


title: SOM-28

description:
CP-D_49
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 68


title: 4.7 - 4.9 week epithelial cell 59


title: SOM-34

description:
CP-D_55
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 57


title: L6Cal-19

description:
CP-R_49
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 56


title: L6Cal-18

description:
CP-R_48
L6Cal-L6Thal_tpm5.txt


title: L6Cal-22

description:
CP-R_51
L6Cal-L6Thal_tpm5.txt


title: SOM-31

description:
CP-D_52
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 52


title: 4.7 - 4.9 week epithelial cell 55


title: 4.7 - 4.9 week epithelial cell 54


title: 4.7 - 4.9 week epithelial cell 51


title: 4.7 - 4.9 week epithelial cell 53


title: PV-70

description:
CP-D_47
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt

value: PV-Cre x Rosa-tdTomato


title: L6Cal-16

description:
CP-R_46
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 50


title: L6Cal-15

description:
CP-R_44
L6Cal-L6Thal_tpm5.txt


title: PV-69

description:
CP-D_46
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 48


title: 4.7 - 4.9 week epithelial cell 49


title: 4.7 - 4.9 week epithelial cell 47


title: L6Cal-20

description:
CP-R_5
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 46


title: 4.7 - 4.9 week epithelial cell 43


title: PV-71

description:
CP-D_48
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: PV-66

description:
CP-D_43
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 42


title: PV-65

description:
CP-D_42
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 44


title: L6Cal-17

description:
CP-R_47
L6Cal-L6Thal_tpm5.txt


title: PV-64

description:
CP-D_41
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 41


title: PV-68

description:
CP-D_45
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: L6Cal-11

description:
CP-R_40
L6Cal-L6Thal_tpm5.txt


title: PV-63

description:
CP-D_40
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 40


title: L6Cal-10

description:
CP-R_4
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 39


title: 4.7 - 4.9 week epithelial cell 36


title: L6Cal-9

description:
CP-R_38
L6Cal-L6Thal_tpm5.txt


title: PV-61

description:
CP-D_37
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 37


title: PV-62

description:
CP-D_38
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: PV-67

description:
CP-D_44
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 34


title: L6Cal-14

description:
CP-R_43
L6Cal-L6Thal_tpm5.txt


title: L6Cal-8

description:
CP-R_37
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 35


title: 4.7 - 4.9 week epithelial cell 45


title: 4.7 - 4.9 week epithelial cell 33


title: 4.7 - 4.9 week epithelial cell 32


title: L6Cal-7

description:
CP-R_36
L6Cal-L6Thal_tpm5.txt


title: L6Cal-12

description:
CP-R_41
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 31


title: PV-59

description:
CP-D_35
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: PV-60

description:
CP-D_36
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: L6Cal-6

description:
CP-R_35
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 38


title: 4.7 - 4.9 week epithelial cell 29


title: PV-58

description:
CP-D_34
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 28


title: PV-57

description:
CP-D_33
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: L6Thal-23

description:
CP-R_33
L6Cal-L6Thal_tpm5.txt


title: PV-56

description:
CP-D_32
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 25


title: 4.7 - 4.9 week epithelial cell 24


title: 4.7 - 4.9 week epithelial cell 21


title: 4.7 - 4.9 week epithelial cell 26


title: PV-55

description:
CP-D_31
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 23


title: L6Thal-22

description:
CP-R_32
L6Cal-L6Thal_tpm5.txt


title: L6Thal-21

description:
CP-R_31
L6Cal-L6Thal_tpm5.txt


title: PV-54

description:
CP-D_30
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 30


title: 4.7 - 4.9 week epithelial cell 20


title: L6Thal-20

description:
CP-R_30
L6Cal-L6Thal_tpm5.txt


title: L6Cal-13

description:
CP-R_42
L6Cal-L6Thal_tpm5.txt


title: PV-53

description:
CP-D_29
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt


title: L6Cal-4

description:
CP-R_3
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 19


title: 4.7 - 4.9 week epithelial cell 17


title: 4.7 - 4.9 week epithelial cell 18


title: L6Thal-19

description:
CP-R_29
L6Cal-L6Thal_tpm5.txt


title: L6Cal-5

description:
CP-R_34
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 16


title: 4.7 - 4.9 week epithelial cell 15


title: 4.7 - 4.9 week epithelial cell 14


title: VIP-40

description:
CP-D_27
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 22


title: 4.7 - 4.9 week epithelial cell 13


title: 4.7 - 4.9 week epithelial cell 12


title: L6Thal-18

description:
CP-R_28
L6Cal-L6Thal_tpm5.txt


title: VIP-39

description:
CP-D_26
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: VIP-38

description:
CP-D_25
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 11


title: 4.7 - 4.9 week epithelial cell 10


title: L6Thal-17

description:
CP-R_27
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 9


title: 4.7 - 4.9 week epithelial cell 27


title: L6Thal-15

description:
CP-R_25
L6Cal-L6Thal_tpm5.txt


title: L6Thal-16

description:
CP-R_26
L6Cal-L6Thal_tpm5.txt


title: VIP-36

description:
CP-D_23
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: L6Thal-14

description:
CP-R_24
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 6


title: VIP-37

description:
CP-D_24
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: L6Thal-13

description:
CP-R_23
L6Cal-L6Thal_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 7


title: 4.7 - 4.9 week epithelial cell 5


title: VIP-35

description:
CP-D_22
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: 4.7 - 4.9 week epithelial cell 3


title: 4.7 - 4.9 week epithelial cell 4


title: 4.7 - 4.9 week epithelial cell 2


title: VIP-33

description:
CP-D_20
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: VIP-34

description:
CP-D_21
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: L6Thal-12

description:
CP-R_22
L6Cal-L6Thal_tpm5.txt


title: 2-week epithelial cell 144

value: Pre-puberty


title: 2-week epithelial cell 142


title: 4.7 - 4.9 week epithelial cell 1


title: VIP-32

description:
CP-D_19
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: 2-week epithelial cell 143


title: L6Thal-11

description:
CP-R_21
L6Cal-L6Thal_tpm5.txt

value: 129S2/SvPasCrl, CD-1 mix


title: 4.7 - 4.9 week epithelial cell 8


title: 2-week epithelial cell 141


title: L6Thal-10

description:
CP-R_20
L6Cal-L6Thal_tpm5.txt

value: postnatal day >p35


title: VIP-31

description:
CP-D_18
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: 2-week epithelial cell 140


title: L6Cal-3

description:
CP-R_2
L6Cal-L6Thal_tpm5.txt

value: layer 6 -> contralateral ctx


title: 2-week epithelial cell 139


title: L6Thal-9

description:
CP-R_19
L6Cal-L6Thal_tpm5.txt


title: VIP-30

description:
CP-D_17
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: VIP-29

description:
CP-D_16
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: 2-week epithelial cell 136


title: 2-week epithelial cell 135


title: 2-week epithelial cell 137


title: 2-week epithelial cell 138


title: L6Thal-7

description:
CP-R_17
L6Cal-L6Thal_tpm5.txt


title: 2-week epithelial cell 133


title: 2-week epithelial cell 134


title: L6Thal-8

description:
CP-R_18
L6Cal-L6Thal_tpm5.txt


title: VIP-28

description:
CP-D_15
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: VIP-41

description:
CP-D_28
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: VIP-27

description:
CP-D_14
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: 2-week epithelial cell 131


title: L6Thal-6

description:
CP-R_16
L6Cal-L6Thal_tpm5.txt


title: 2-week epithelial cell 132


title: VIP-26

description:
CP-D_13
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: 2-week epithelial cell 130


title: L6Thal-4

description:
CP-R_14
L6Cal-L6Thal_tpm5.txt


title: 2-week epithelial cell 128


title: 2-week epithelial cell 127


title: 2-week epithelial cell 129


title: 2-week epithelial cell 126


title: 2-week epithelial cell 125


title: L6Thal-3

description:
CP-R_13
L6Cal-L6Thal_tpm5.txt


title: 2-week epithelial cell 124


title: L6Thal-2

description:
CP-R_12
L6Cal-L6Thal_tpm5.txt


title: L6Thal-1

description:
CP-R_11
L6Cal-L6Thal_tpm5.txt


title: 2-week epithelial cell 123


title: 2-week epithelial cell 121


title: VIP-24

description:
CP-D_11
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: VIP-23

description:
CP-D_10
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: PV-51

description:
CP-C_59
SOM-PV_tpm5.txt


title: 2-week epithelial cell 118


title: 2-week epithelial cell 119


title: L6Cal-2

description:
CP-R_10
L6Cal-L6Thal_tpm5.txt


title: 2-week epithelial cell 122


title: L6Cal-1

description:
CP-R_1
L6Cal-L6Thal_tpm5.txt


title: 2-week epithelial cell 116


title: PV-49

description:
CP-C_57
SOM-PV_tpm5.txt


title: 2-week epithelial cell 117


title: PV-52

description:
CP-C_60
SOM-PV_tpm5.txt


title: 2-week epithelial cell 120


title: VIP-25

description:
CP-D_12
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt


title: PV-50

description:
CP-C_58
SOM-PV_tpm5.txt


title: L6Thal-5

description:
CP-R_15
L6Cal-L6Thal_tpm5.txt


title: CA1V-37

description:
CP-O_90
CA1d-CA1v_tpm5.txt

source_name: hippocampus

value: ventral hippocampus CA1


title: PV-48

description:
CP-C_56
SOM-PV_tpm5.txt


title: 2-week epithelial cell 114


title: CA1V-36

description:
CP-O_89
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 115


title: 2-week epithelial cell 113


title: PV-47

description:
CP-C_55
SOM-PV_tpm5.txt


title: CA1V-35

description:
CP-O_88
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 110


title: PV-46

description:
CP-C_54
SOM-PV_tpm5.txt


title: PV-45

description:
CP-C_53
SOM-PV_tpm5.txt


title: CA1V-33

description:
CP-O_84
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 105


title: PV-44

description:
CP-C_52
SOM-PV_tpm5.txt


title: CA1V-32

description:
CP-O_83
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 109


title: CA1V-31

description:
CP-O_82
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 106


title: 2-week epithelial cell 104


title: 2-week epithelial cell 103


title: PV-43

description:
CP-C_51
SOM-PV_tpm5.txt


title: 2-week epithelial cell 101


title: CA1V-30

description:
CP-O_81
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 102


title: PV-41

description:
CP-C_49
SOM-PV_tpm5.txt


title: 2-week epithelial cell 100


title: CA1V-29

description:
CP-O_79
CA1d-CA1v_tpm5.txt


title: CA1D-42

description:
CP-O_8
CA1d-CA1v_tpm5.txt

value: dorsal hippocampus CA1


title: 2-week epithelial cell 99

value: FVB/NJ


title: 2-week epithelial cell 111


title: 2-week epithelial cell 97


title: 2-week epithelial cell 98


title: CA1V-34

description:
CP-O_85
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 108


title: 2-week epithelial cell 112


title: 2-week epithelial cell 107


title: 2-week epithelial cell 95


title: PV-38

description:
CP-C_46
SOM-PV_tpm5.txt

value: c57bl6, CD-1 mix


title: PV-39

description:
CP-C_47
SOM-PV_tpm5.txt

value: postnatal day >p21


title: 2-week epithelial cell 96


title: CA1V-27

description:
CP-O_77
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 94


title: 2-week epithelial cell 92


title: 2-week epithelial cell 93


title: 2-week epithelial cell 91


title: PV-37

description:
CP-C_45
SOM-PV_tpm5.txt


title: PV-36

description:
CP-C_44
SOM-PV_tpm5.txt


title: CA1V-26

description:
CP-O_76
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 89


title: 2-week epithelial cell 90


title: PV-42

description:
CP-C_50
SOM-PV_tpm5.txt


title: 2-week epithelial cell 88


title: PV-40

description:
CP-C_48
SOM-PV_tpm5.txt


title: PV-35

description:
CP-C_43
SOM-PV_tpm5.txt


title: 2-week epithelial cell 86


title: CA1V-24

description:
CP-O_73
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 87


title: PV-34

description:
CP-C_42
SOM-PV_tpm5.txt


title: 2-week epithelial cell 85


title: PV-33

description:
CP-C_41
SOM-PV_tpm5.txt


title: CA1V-23

description:
CP-O_72
CA1d-CA1v_tpm5.txt


title: CA1V-28

description:
CP-O_78
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 84


title: 2-week epithelial cell 83


title: PV-32

description:
CP-C_40
SOM-PV_tpm5.txt


title: CA1V-25

description:
CP-O_74
CA1d-CA1v_tpm5.txt


title: CA1V-22

description:
CP-O_71
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 82


title: CA1V-21

description:
CP-O_70
CA1d-CA1v_tpm5.txt


title: PV-31

description:
CP-C_38
SOM-PV_tpm5.txt


title: 2-week epithelial cell 81


title: CA1D-41

description:
CP-O_69
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 80


title: 2-week epithelial cell 79


title: 2-week epithelial cell 78


title: PV-29

description:
CP-C_36
SOM-PV_tpm5.txt


title: CA1D-40

description:
CP-O_68
CA1d-CA1v_tpm5.txt


title: PV-30

description:
CP-C_37
SOM-PV_tpm5.txt


title: 2-week epithelial cell 77


title: 2-week epithelial cell 76


title: PV-28

description:
CP-C_35
SOM-PV_tpm5.txt


title: CA1D-38

description:
CP-O_65
CA1d-CA1v_tpm5.txt


title: PV-27

description:
CP-C_34
SOM-PV_tpm5.txt


title: 2-week epithelial cell 74


title: 2-week epithelial cell 73


title: 2-week epithelial cell 72


title: 2-week epithelial cell 75


title: 2-week epithelial cell 71


title: PV-26

description:
CP-C_33
SOM-PV_tpm5.txt


title: 2-week epithelial cell 70


title: 2-week epithelial cell 69


title: CA1D-36

description:
CP-O_62
CA1d-CA1v_tpm5.txt


title: PV-25

description:
CP-C_32
SOM-PV_tpm5.txt


title: 2-week epithelial cell 68


title: 2-week epithelial cell 67


title: CA1D-35

description:
CP-O_61
CA1d-CA1v_tpm5.txt


title: CA1V-20

description:
CP-O_60
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 65


title: 2-week epithelial cell 64


title: CA1D-39

description:
CP-O_66
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 66


title: PV-23

description:
CP-C_30
SOM-PV_tpm5.txt


title: CA1V-19

description:
CP-O_59
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 62


title: 2-week epithelial cell 61


title: CA1D-37

description:
CP-O_64
CA1d-CA1v_tpm5.txt


title: PV-24

description:
CP-C_31
SOM-PV_tpm5.txt


title: 2-week epithelial cell 60


title: PV-22

description:
CP-C_29
SOM-PV_tpm5.txt


title: PV-20

description:
CP-C_27
SOM-PV_tpm5.txt


title: CA1D-34

description:
CP-O_6
CA1d-CA1v_tpm5.txt


title: CA1V-17

description:
CP-O_57
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 59


title: 2-week epithelial cell 63


title: CA1V-16

description:
CP-O_56
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 55


title: 2-week epithelial cell 57


title: 2-week epithelial cell 58


title: 2-week epithelial cell 56


title: PV-18

description:
CP-C_25
SOM-PV_tpm5.txt


title: CA1V-15

description:
CP-O_55
CA1d-CA1v_tpm5.txt


title: PV-17

description:
CP-B_90
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: 2-week epithelial cell 52


title: 2-week epithelial cell 53


title: 2-week epithelial cell 51


title: 2-week epithelial cell 50


title: CA1V-13

description:
CP-O_53
CA1d-CA1v_tpm5.txt


title: SOM-27

description:
CP-B_9
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1V-18

description:
CP-O_58
CA1d-CA1v_tpm5.txt


title: PV-21

description:
CP-C_28
SOM-PV_tpm5.txt


title: 2-week epithelial cell 49


title: PV-16

description:
CP-B_89
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: 2-week epithelial cell 48


title: 2-week epithelial cell 46


title: 2-week epithelial cell 45


title: 2-week epithelial cell 47


title: PV-19

description:
CP-C_26
SOM-PV_tpm5.txt


title: PV-14

description:
CP-B_86
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: 2-week epithelial cell 44


title: 2-week epithelial cell 43


title: CA1D-33

description:
CP-O_5
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 54


title: PV-13

description:
CP-B_85
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1V-10

description:
CP-O_50
CA1d-CA1v_tpm5.txt


title: CA1V-14

description:
CP-O_54
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 41


title: 2-week epithelial cell 40


title: 2-week epithelial cell 38


title: PV-11

description:
CP-B_83
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: 2-week epithelial cell 39


title: CA1V-8

description:
CP-O_48
CA1d-CA1v_tpm5.txt


title: CA1V-11

description:
CP-O_51
CA1d-CA1v_tpm5.txt


title: PV-15

description:
CP-B_87
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1V-7

description:
CP-O_47
CA1d-CA1v_tpm5.txt


title: CA1V-12

description:
CP-O_52
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 37


title: PV-10

description:
CP-B_82
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: 2-week epithelial cell 35


title: PV-9

description:
CP-B_81
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: 2-week epithelial cell 33


title: PV-12

description:
CP-B_84
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: PV-8

description:
CP-B_80
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: 2-week epithelial cell 42


title: SOM-26

description:
CP-B_8
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: 2-week epithelial cell 31


title: CA1V-6

description:
CP-O_46
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 30


title: PV-7

description:
CP-B_79
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1V-5

description:
CP-O_45
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 36


title: 2-week epithelial cell 29


title: CA1V-9

description:
CP-O_49
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 32


title: CA1V-3

description:
CP-O_43
CA1d-CA1v_tpm5.txt


title: CA1V-4

description:
CP-O_44
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 26


title: 2-week epithelial cell 25


title: 2-week epithelial cell 34


title: CA1V-1

description:
CP-O_41
CA1d-CA1v_tpm5.txt


title: PV-5

description:
CP-B_77
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: PV-6

description:
CP-B_78
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: PV-4

description:
CP-B_76
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1V-2

description:
CP-O_42
CA1d-CA1v_tpm5.txt


title: CA1D-32

description:
CP-O_40
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 21


title: CA1D-31

description:
CP-O_4
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 28


title: PV-3

description:
CP-B_75
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: 2-week epithelial cell 20


title: 2-week epithelial cell 19


title: PV-2

description:
CP-B_74
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1D-30

description:
CP-O_38
CA1d-CA1v_tpm5.txt


title: PV-1

description:
CP-B_73
SOM-PV_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1D-29

description:
CP-O_37
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 16


title: 2-week epithelial cell 17


title: 2-week epithelial cell 27


title: 2-week epithelial cell 15


title: VIP-22

description:
CP-B_71
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt

value: VIP-Cre x Rosa-tdTomato


title: 2-week epithelial cell 23


title: 2-week epithelial cell 18


title: 2-week epithelial cell 24


title: 2-week epithelial cell 22


title: 2-week epithelial cell 13


title: VIP-21

description:
CP-B_70
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt

value: visual cortex layer 2/3


title: 2-week epithelial cell 12

value: Total epithelium


title: CA1D-27

description:
CP-O_35
CA1d-CA1v_tpm5.txt

value: SepW1-Cre, WT


title: 2-week epithelial cell 11


title: SOM-25

description:
CP-B_7
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: VIP-20

description:
CP-B_69
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: 2-week epithelial cell 10


title: 2-week epithelial cell 8


title: 2-week epithelial cell 7


title: 2-week epithelial cell 9


title: CA1D-25

description:
CP-O_33
CA1d-CA1v_tpm5.txt


title: VIP-19

description:
CP-B_68
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1D-24

description:
CP-O_32
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 14


title: CA1D-28

description:
CP-O_36
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 6


title: VIP-17

description:
CP-B_66
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: VIP-18

description:
CP-B_67
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1D-23

description:
CP-O_31
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 4


title: 2-week epithelial cell 1


title: VIP-15

description:
CP-B_64
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 88

data_processing:
RNA-seq reads were mapped to the mouse genome using the align function of Rsubread version 1.15.9
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's built-in NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

value: Adult

value: Luminal

tag: pcr plate

value: C


title: CA1D-21

description:
CP-O_29
CA1d-CA1v_tpm5.txt


title: CA1D-20

description:
CP-O_28
CA1d-CA1v_tpm5.txt


title: 2-week epithelial cell 5


title: 2-week epithelial cell 3


title: VIP-16

description:
CP-B_65
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1D-26

description:
CP-O_34
CA1d-CA1v_tpm5.txt


title: Adult luminal cell 90


title: Adult luminal cell 89


title: 2-week epithelial cell 2


title: VIP-14

description:
CP-B_63
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 87


title: Adult luminal cell 86


title: VIP-13

description:
CP-B_62
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 84


title: CA1D-18

description:
CP-O_26
CA1d-CA1v_tpm5.txt


title: CA1D-19

description:
CP-O_27
CA1d-CA1v_tpm5.txt


title: Adult luminal cell 85


title: Adult luminal cell 83


title: VIP-12

description:
CP-B_61
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1D-17

description:
CP-O_25
CA1d-CA1v_tpm5.txt


title: CA1D-22

description:
CP-O_3
CA1d-CA1v_tpm5.txt


title: Adult luminal cell 81


title: Adult luminal cell 82


title: Adult luminal cell 80


title: CA1D-16

description:
CP-O_24
CA1d-CA1v_tpm5.txt


title: Adult luminal cell 79


title: SOM-24

description:
CP-B_6
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt

value: SOM-Cre x Rosa-tdTomato


title: Adult luminal cell 78


title: VIP-10

description:
CP-B_59
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 76


title: VIP-9

description:
CP-B_58
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 74


title: CA1D-14

description:
CP-O_22
CA1d-CA1v_tpm5.txt


title: CA1D-15

description:
CP-O_23
CA1d-CA1v_tpm5.txt


title: CA1D-13

description:
CP-O_21
CA1d-CA1v_tpm5.txt


title: VIP-11

description:
CP-B_60
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 73


title: VIP-8

description:
CP-B_57
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 71


title: Adult luminal cell 69


title: CA1D-12

description:
CP-O_20
CA1d-CA1v_tpm5.txt


title: CA1D-11

description:
CP-O_19
CA1d-CA1v_tpm5.txt


title: Adult luminal cell 70


title: VIP-6

description:
CP-B_55
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 68


title: CA1D-10

description:
CP-O_18
CA1d-CA1v_tpm5.txt


title: VIP-7

description:
CP-B_56
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 67


title: VIP-5

description:
CP-B_54
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 66


title: CA1D-9

description:
CP-O_17
CA1d-CA1v_tpm5.txt


title: Adult luminal cell 65


title: VIP-4

description:
CP-B_53
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 75


title: Adult luminal cell 64


title: VIP-3

description:
CP-B_52
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1D-8

description:
CP-O_16
CA1d-CA1v_tpm5.txt


title: Adult luminal cell 63


title: VIP-2

description:
CP-B_51
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 62


title: CA1D-7

description:
CP-O_15
CA1d-CA1v_tpm5.txt


title: Adult luminal cell 61


title: Adult luminal cell 59


title: CA1D-6

description:
CP-O_14
CA1d-CA1v_tpm5.txt


title: VIP-1

description:
CP-B_50
SOM-VIP_tpm5.txt
PV-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 60


title: Adult luminal cell 58


title: CA1D-5

description:
CP-O_13
CA1d-CA1v_tpm5.txt


title: Adult luminal cell 57


title: SOM-23

description:
CP-B_5
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 55


title: CA1D-4

description:
CP-O_12
CA1d-CA1v_tpm5.txt


title: Adult luminal cell 56


title: Adult luminal cell 54


title: SOM-22

description:
CP-B_4
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1D-3

description:
CP-O_11
CA1d-CA1v_tpm5.txt


title: SOM-21

description:
CP-B_30
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: CA1D-2

description:
CP-O_10
CA1d-CA1v_tpm5.txt


title: Adult luminal cell 53


title: Adult luminal cell 51


title: SOM-20

description:
CP-B_3
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 50


title: CA1D-1

description:
CP-O_1
CA1d-CA1v_tpm5.txt


title: Adult luminal cell 48


title: Adult luminal cell 49


title: SOM-19

description:
CP-B_29
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: SOM-18

description:
CP-B_28
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 47


title: TAMR_siGRHL2C-3_KC-S9_Rep2

city: Durham

first: Jeff

last: Jasper

state: NC

department: Pharmacology and Cancer Biology

institute: Duke University

data_processing:
Aligned using STARv2.5.2b
Gene/Transcript counts were using Salmonv0.8.0 from BAMs
Data were normalized using DESeq2
Genome_build: hg19

organism: Homo sapiens

source_name: MCF7-derived 4-OHT resistant cell line

growth_protocol: phenol red free DMEM/F12 with 8% charcoal stripped FBS, supplemented with NaPyr and NEAA

extract_protocol:
polyA-RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Harvested 72 hours post-transfection.

tag: cell line

value: TAMR

tag: sirna

tag: replicate


title: TAMR_siGRHL2C-3_KC-S9_Rep1


title: Adult luminal cell 46

tag: strain

tag: age


title: Adult luminal cell 45


title: SOM-17

description:
CP-B_27
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt

tag: genotype

tag: position


title: TAMR_siGRHL2C-2_KC-S6_Rep2


title: Adult luminal cell 44


title: SOM-16

description:
CP-B_26
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: TAMR_siGRHL2C-2_KC-S6_Rep1


title: Adult luminal cell 52


title: SOM-15

description:
CP-B_25
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: TAMR_siGRHL2C-1_KC-S3_Rep2


title: Adult luminal cell 41


title: Adult luminal cell 40


title: SOM-14

description:
CP-B_24
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 39


title: Adult luminal cell 37


title: Adult luminal cell 38


title: Adult luminal cell 36


title: TAMR_siGRHL2A-3_KC-S8_Rep2


title: TAMR_siGRHL2A-3_KC-S8_Rep1


title: SOM-12

description:
CP-B_22
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 33


title: Adult luminal cell 34


title: SOM-13

description:
CP-B_23
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 32


title: SOM-11

description:
CP-B_21
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 43


title: Adult luminal cell 35


title: SOM-10

description:
CP-B_20
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 42


title: TAMR_siGRHL2A-2_KC-S5_Rep2


title: Adult luminal cell 30


title: TAMR_siGRHL2A-2_KC-S5_Rep1


title: Adult luminal cell 29


title: Adult luminal cell 28


title: SOM-9

description:
CP-B_19
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: TAMR_siGRHL2C-1_KC-S3_Rep1


title: Adult luminal cell 27


title: TAMR_siGRHL2A-1_KC-S2_Rep2


title: TAMR_siGRHL2A-1_KC-S2_Rep1


title: SOM-8

description:
CP-B_18
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 26


title: Adult luminal cell 25


title: TAMR_siCtrl-3_KC-S7_Rep2

value: siCtrl


title: SOM-6

description:
CP-B_16
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 24

value: B


title: Adult luminal cell 23


title: TAMR_siCtrl-3_KC-S7_Rep1


title: TAMR_siCtrl-2_KC-S4_Rep2


title: Adult luminal cell 31


title: Adult luminal cell 21


title: SOM-5

description:
CP-B_15
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 22


title: Adult luminal cell 19


title: SOM-4

description:
CP-B_14
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 20


title: Adult luminal cell 18


title: SOM-3

description:
CP-B_13
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 17


title: Adult luminal cell 16


title: TAMR_siCtrl-1_KC-S1_Rep2


title: Adult luminal cell 15


title: TAMR_siCtrl-2_KC-S4_Rep1


title: TAMR_siCtrl-1_KC-S1_Rep1


title: SOM-2

description:
CP-B_11
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: SOM-7

description:
CP-B_17
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 14


title: SOM-1

description:
CP-B_10
SOM-PV_tpm5.txt
SOM-VIP_tpm5.txt
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: Adult luminal cell 12


title: Adult luminal cell 13


title: Adult luminal cell 10


title: Adult luminal cell 11


title: Adult luminal cell 9


title: WS8V_2

description: MCF7-derived 4-OHT sensitive

data_processing:
Aligned using STARv2.5.2b
Gene/Transcript counts were using Salmonv0.8.0 from BAMs
Data were normalized using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: counts

treatment_protocol: 2 days in media, 24hrs hormone treatment

value: VEH

tag: treatment time


title: WS8V_1

description: MCF7-derived 4-OHT sensitive


title: WS8T_2

description: MCF7-derived 4-OHT sensitive


title: Adult luminal cell 6


title: TAMRV_2

description: MCF7-derived 4-OHT resistant

source_name: TAMR


title: Adult luminal cell 4


title: Adult luminal cell 5


title: Adult luminal cell 3


title: Adult luminal cell 7


title: Adult luminal cell 2


title: WS8T_1

description: MCF7-derived 4-OHT sensitive


title: Adult basal cell 96

value: Basal


title: TAMRV_1

description: MCF7-derived 4-OHT resistant


title: Adult luminal cell 1


title: Adult basal cell 95


title: Adult basal cell 94


title: Adult basal cell 93


title: TAMRT_1

description: MCF7-derived 4-OHT resistant


title: MCF7V_2


title: Adult basal cell 92


title: Adult basal cell 91


title: Drosophila ananassae female body small RNA [M044_dana_female_body]

description: female bodies

organism: Drosophila ananassae

source_name: D. ananassae female body small RNA

tag: tissue

value: abdomen and thorax


title: Adult basal cell 90

value: FVB/NJ


title: Drosophila pseudoobscura head small RNA [M062_dpse_head]

description: heads

organism: Drosophila pseudoobscura

source_name: D. pseudoobscura head small RNA

value: head


title: Adult basal cell 89


title: Drosophila pseudoobscura embryo small RNA [M059_dpse_embryo]

description: mixed embryos

source_name: D. pseudoobscura embryo small RNA

value: whole embryo


title: MCF7V_1


title: Adult basal cell 86


title: MCF7T_1


title: Drosophila pseudoobscura female body small RNA [M040_dpse_female_body]

description: female bodies

source_name: D. pseudoobscura female body small RNA


title: Adult basal cell 88


title: Adult luminal cell 72


title: Adult basal cell 87


title: Adult basal cell 84


title: Adult basal cell 82


title: MCF7T_2


title: Adult basal cell 85


title: Drosophila ananassae embryo small RNA [M058_dana_embryo]

description: mixed embryos

source_name: D. ananassae embryo small RNA


title: TAMRT_2

description: MCF7-derived 4-OHT resistant


title: Drosophila ananassae embryo small RNA [V039_dana_embryo]

description: mixed embryos


title: Adult basal cell 81


title: Drosophila pseudoobscura male body small RNA [M022_dpse_male_body]

description: male bodies

source_name: D. pseudoobscura male body small RNA


title: Naïve_2

city: Tokyo

first: Seiji

last: Shiozawa

address: 35 Shinanomachi, Shinjuku-ku

country: Japan

institute: Keio University, School of Medicine

data_processing:
Base-calling and chastity ﬁltering were performed using Real-Time Analysis Software version 1.18.61.
The resulting reads were mapped to the UCSC human genome 19 using sailfish version 0.7.6 with default setting.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Naïve-like state hiPSC

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit.
Poly(A)+ RNA was selected and converted to a library of cDNA fragments (200–250 bp) with adaptors attached to both ends for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit Set [Illumina] as per the manufacturer’s instructions.

tag: cell type

value: hiPSC

tag: cell state

value: Naïve-like


title: Naïve_1


title: Drosophila ananassae head small RNA [V055_dana_head]

description: heads

source_name: D. ananassae head small RNA


title: Drosophila ananassae head small RNA [V106_dana_head]

description: heads


title: Adult basal cell 79


title: Adult luminal cell 8


title: Adult basal cell 78


title: Adult basal cell 77


title: Adult basal cell 76


title: Primed_2

source_name: Primed state hiPSC

value: Primed


title: Adult basal cell 75


title: Adult basal cell 83


title: Naïve_3


title: Adult basal cell 74


title: Adult basal cell 71


title: Drosophila sechellia embryo small RNA [V114_dsec_embryo]

description: mixed embryos

source_name: D. sechellia embryo small RNA


title: Adult basal cell 72


title: Drosophila mojavensis female body small RNA [M046_dmo_female_body]

description: female bodies

source_name: D. mojavensis female body small RNA


title: Erythroid cells fixed with 5% formaldehyde replicate 2

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
P5Rep2
3C library preparation followed by double oligonucleotide capture

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

source_name: Primary erythroid cells

growth_protocol: Ter-119+ erythroid cells were obtained from the spleens of female C57BL/6 mice treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days).

extract_protocol:
Spleens were gently dissociated into a single cell suspension and cells were passed through a 70 μm strainer to remove clumps. For ter-119+ cell selection, cells were stained with phycoerythrin conjugated anti-ter-119 antibodies and positively selected using anti-phycoerythrin MACS beads before fixation with formaldehyde.
The Capture-C technologies combine 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Detailed description follows. The protocol used for the generation of the 3C libraries was similar to other 3C-based methods. Briefly, cells were crosslinked with 2% formaldehyde (this was varied for the reduced crosslinking experiments), quenched with cold glycine, washed in phosphate buffered saline, resuspended in cold lysis buffer and snap frozen to -80. Cells were thawed on ice, washed in Milli-Q dH2O and Dounce homogenized on ice. Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37 °C for 1h at 1400 rpm on a Thermomixer, followed by a further incubation of 1h after the addition of Triton X-100 (final concentration 1.67%). An overnight digestion was performed using DpnII (final concentration 500U/ml; 37 °C / 1400 rpm). The digested chromatin was ligated overnight using T4 DNA HC ligase (final concentration 10U/ml; 16 °C / 1400 rpm). The samples were de-crosslinked overnight with Proteinase K at 65 °C, followed by a 30 min incubation at 37 °C with RNAse. A Phenol/Chloroform extraction was performed, followed by an ethanol precipitation and wash. Digestion efficiencies were assessed by gel electrophoresis and RT-PCR, which showed digestion efficiencies higher than 80%. The DNA contents of the DpnII 3C libraries were quantitated using a Qubit fluorometer. Different strategies were used for the sequencing library preparation. For the low-input experiments, the LI Capture-C or Tag-Capture-C protocol was used, for which 50-200 ng of DNA was adapter ligated using a strategy based on sonication combined with the NEBNext Ultra DNA Library Prep kit, or the Illumina Nextera DNA Library Prep kit, respectively. For the reduced cross-linking experiments, the NG Capture-C protocol was used, for which 5 ug of DNA was adapter ligated using a strategy based on sonication combined with the NEBNext DNA Library Prep kit. The quality of the libraries was assessed using the Agilent ScreenTape system. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. 700 ng-2 ug of the adapter ligated libraries was hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resulting captured library was assessed using the Agilent ScreenTape system. The libraries were sequenced using the Illumina MiSeq (150bp paired end reads) platform.

value: Ter-119+ cells isolated from phenylhydrazine treated spleen

tag: genes analysed

tag: molecule subtype

value: Next generation Capture-C products


title: Primed_1


title: Adult basal cell 70

value: Adult


title: Adult basal cell 69


title: Adult basal cell 68


title: Drosophila erecta head small RNA [V060_dere_head]

description: heads

source_name: D. erecta head small RNA


title: Erythroid cells fixed with 5% formaldehyde replicate 1

description:
P5Rep1
3C library preparation followed by double oligonucleotide capture


title: Adult basal cell 80

source_name: mammary gland


title: Primed_3


title: Adult basal cell 67


title: Drosophila erecta embryo small RNA [V040_dere_embryo]

description: mixed embryos

source_name: D. erecta embryo small RNA


title: Drosophila ananassae male body small RNA [V105_dana_male_body]

description: male bodies

source_name: D. ananassae male body small RNA


title: Adult basal cell 66


title: Erythroid cells fixed with 4% formaldehyde replicate 2

description:
P4Rep2
3C library preparation followed by double oligonucleotide capture


title: Erythroid cells fixed with 4% formaldehyde replicate 1

description:
P4Rep1
3C library preparation followed by double oligonucleotide capture


title: Drosophila mojavensis embryo small RNA [M060_dmo_embryo]

description: mixed embryos

source_name: D. mojavensis embryo small RNA


title: Adult basal cell 64


title: Adult basal cell 73


title: Adult basal cell 63


title: Erythroid cells fixed with 3% formaldehyde replicate 2

description:
P3Rep2
3C library preparation followed by double oligonucleotide capture


title: Drosophila erecta head small RNA [V108_dere_head]

description: heads


title: C6

city: Rosario

first: Edgardo

middle: Gabriel

last: Bresso

state: Santa Fe

address: Ocampo y Esmeralda, Predio CONICET-Rosario

country: Argentina

institute: IBR-CONICET

description:
C6.fastq
4KO_B3

data_processing:
Resulting RNA-Seq raw data was processed as described elsewhere (Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W, Robinson MD. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc. 2013 Sep;8(9):1765-86. doi: 10.1038/nprot.2013.099.) and differential expression assessed with edgeR v.3.8.6 (Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139-140. doi:10.1093/bioinformatics/btp616.).
Genome_build: TAIR10
Supplementary_files_format_and_content: raw counts of features (genes) generated with HTSeq-count v.0.7.2 (Anders S, Pyl TP, Huber W. HTSeq -- A Python framework to work with high-throughput sequencing data. bioRxiv 2014. doi: 10.1101/002824.) from reads aligned to the Arabidopsis TAIR10 genome with TopHat2 v.2.0.13 (Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013 Apr 25;14(4):R36. doi: 10.1186/gb-2013-14-4-r36.)

organism: Arabidopsis thaliana

growth_protocol: For this experiment seeds were surface sterilized sown on plates with MS-Agar medium and stratified for at least 2 days. To synchronize the developmental stage of the three genotypes at tissue collection, an offset of 2 days was generated before placing in the greenhouse the plates of the next plant line, starting with tcp2 tcp3 tcp4 tcp10 and ending with Col-0. Once in the greenhouse, plates were grown at 23°C in long day conditions (16h light/8h dark) for 5 days, at which point seedlings were transplanted to individual soil pots.

extract_protocol:
Total RNA was extracted using TRIzol™ (Invitrogen #15596-018), treated with Turbo™ DNase (Ambion #AM2238), and re-purified by Phenol-Chloroform-Isoamyl Alcohol (25:24:1, v/v) extraction.
Barcoded libraries were constructed using the Illumina TruSeq™ RNA kit with an average of 1 ug of total RNA as starting material.

treatment_protocol: At emergence of the 7th leaf, the 5th leaf of each plant was harvested at Zeitgeber time (ZT) 6, dissected on a cold plate into “Center” and “Margin” samples. Each “Center” and “Margin” sample replicate consisted of the center and margin portions respectively of the 5th leaf of 15-20 different individual plants.

value: tcp2-tcp3-tcp4-tcp10 mutant

value: leaf

tag: tissue compartment

value: Center

tag: repetition


title: Adult basal cell 62

tag: cell source


title: Drosophila sechellia head small RNA [V115_dsec_head]

description: heads

source_name: D. sechellia head small RNA


title: Adult basal cell 61

tag: pcr plate


title: Adult basal cell 60

value: A


title: C4

description:
C4.fastq
4KO_B2


title: Erythroid cells fixed with 3% formaldehyde replicate 1

description:
P3Rep1
3C library preparation followed by double oligonucleotide capture


title: Adult basal cell 59


title: Adult basal cell 58


title: Adult basal cell 57


title: Adult basal cell 65

value: B


title: Adult basal cell 55


title: 50 ng of erytrhoid 3C library processed with Tag-Capture-C protocol replicate 2

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
50-Tagm2_S2

data_processing:
Library strategy: Capture-C
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

treatment_protocol: Ter-119+ erythroid cells were obtained from the spleens of female C57BL/6 mice treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days).


title: 50 ng of erytrhoid 3C library processed with Tag-Capture-C protocol replicate 1

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
50-Tagm1_S1


title: Adult basal cell 56


title: 50 ng of erytrhoid 3C library processed with Tag-Capture-C protocol replicate 3

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
50-Tagm3_S3


title: C2

description:
C2.fastq
4KO_B1


title: C3

description:
C3.fastq
4KO_M2

value: Margin


title: Adult basal cell 53

value: Basal


title: Adult basal cell 52


title: C1

description:
C1.fastq
4KO_M1


title: 100 ng of erytrhoid 3C library processed with Tag-Capture-C protocol replicate 2

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
100-Tagm2_S5


title: Adult basal cell 49


title: C5

description:
C5.fastq
4KO_M3


title: 100 ng of erytrhoid 3C library processed with Tag-Capture-C protocol replicate 1

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
100-Tagm1_S4


title: B6

description:
B6.fastq
2KO_B3

value: tcp2-tcp4 mutant


title: Adult basal cell 48

value: FVB/NJ


title: B5

description:
B5.fastq
2KO_M3


title: 200 ng of erytrhoid 3C library processed with Tag-Capture-C protocol replicate 3

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
200_Tagm_Rep3_S3


title: Adult basal cell 46


title: Adult basal cell 45


title: 200 ng of erytrhoid 3C library processed with Tag-Capture-C protocol replicate 2

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
200_Tagm_Rep2_S2


title: Adult basal cell 54


title: B2

description:
B2.fastq
2KO_B1


title: B3

description:
B3.fastq
2KO_M2


title: Adult basal cell 42


title: Adult basal cell 44


title: 50 ng of erytrhoid 3C library processed with LI Capture-C protocol replicate 3

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
50-Ult3_S3


title: Adult basal cell 41


title: Adult basal cell 47


title: 100 ng of erytrhoid 3C library processed with Tag-Capture-C protocol replicate 3

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
100-Tagm3_S6


title: Adult basal cell 40


title: Adult basal cell 43


title: Adult basal cell 50


title: Adult basal cell 39


title: Adult basal cell 51


title: Adult basal cell 38


title: Adult basal cell 37


title: Adult basal cell 36


title: B4

description:
B4.fastq
2KO_B2


title: Adult basal cell 35


title: A5

description:
A5.fastq
Col0_M3


title: 50 ng of erytrhoid 3C library processed with LI Capture-C protocol replicate 2

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
50-Ult2_S2


title: Adult basal cell 34


title: 100 ng of erytrhoid 3C library processed with LI Capture-C protocol replicate 3

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
100-Ult3_S6


title: 200 ng of erytrhoid 3C library processed with Tag-Capture-C protocol replicate 1

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
200_Tagm_Rep1_S1


title: 50 ng of erytrhoid 3C library processed with LI Capture-C protocol replicate 1

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
50-Ult1_S1


title: Adult basal cell 33


title: 100 ng of erytrhoid 3C library processed with LI Capture-C protocol replicate 2

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
100-Ult2_S5


title: A4

description:
A4.fastq
Col0_B2


title: A3

description:
A3.fastq
Col0_M2


title: Adult basal cell 32


title: B1

description:
B1.fastq
2KO_M1


title: Adult basal cell 31


title: Adult basal cell 29


title: 200 ng of erytrhoid 3C library processed with LI Capture-C protocol replicate 3

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
200_Ultra_Rep3_S3


title: A2

description:
A2.fastq
Col0_B1


title: Adult basal cell 30


title: Adult basal cell 28


title: A1

description:
A1.fastq
Col0_M1


title: Adult basal cell 27


title: A6

description:
A6.fastq
Col0_B3


title: 200 ng of erytrhoid 3C library processed with LI Capture-C protocol replicate 2

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
200_Ultra_Rep2_S2


title: Adult basal cell 26


title: Drosophila simulans female body small RNA [M053_dsim_female_body]

description: female bodies

organism: Drosophila simulans

source_name: D. simulans female body small RNA

value: abdomen and thorax


title: Adult basal cell 25


title: 200 ng of erytrhoid 3C library processed with LI Capture-C protocol replicate 1

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
200_Ultra_Rep1_S1


title: Drosophila simulans embryo small RNA [M025_dsim_embryo]

description: mixed embryos

source_name: D. simulans embryo small RNA

value: whole embryo


title: Adult basal cell 24


title: Erythroid cells fixed with 2% formaldehyde replicate 2

description:
3C library preparation followed by double oligonucleotide capture
fixation_alpha.gfc
fixation_beta.gfc
fixation_slc25a37.gfc
2P2_S5_L001


title: Adult basal cell 23


title: Drosophila simulans head small RNA [M023_dsim_head]

description: heads

source_name: D. simulans head small RNA

value: head


title: Adult basal cell 21


title: Adult basal cell 22


title: Erythroid cells fixed with 2% formaldehyde replicate 1

description:
3C library preparation followed by double oligonucleotide capture
fixation_alpha.gfc
fixation_beta.gfc
fixation_slc25a37.gfc
2P1_S1_L001


title: Adult basal cell 19


title: 100 ng of erytrhoid 3C library processed with LI Capture-C protocol replicate 1

description:
3C library preparation followed by double oligonucleotide capture
small_cell_nr_alpha_gfc.txt
small_cell_nr_beta_gfc.txt
small_cell_nr_slc25a37_gfc.txt
100-Ult1_S4


title: Erythroid cells fixed with 1% formaldehyde replicate 2

description:
3C library preparation followed by double oligonucleotide capture
fixation_alpha.gfc
fixation_beta.gfc
fixation_slc25a37.gfc
1P2_S6_L001


title: Drosophila virilis female body small RNA [M047_dvir_female_body]

description: female bodies

source_name: D. virilis female body small RNA


title: Adult basal cell 17


title: Adult basal cell 20


title: Adult basal cell 18


title: Adult basal cell 16


title: Drosophila virilis head small RNA [M028_dvir_head]

description: heads

source_name: D. virilis head small RNA


title: Adult basal cell 15


title: Drosophila virilis embryo small RNA [M061_dvir_embryo]

description: mixed embryos

source_name: D. virilis embryo small RNA


title: Drosophila virilis male body small RNA [M027_dvir_male_body]

description: male bodies

source_name: D. virilis male body small RNA


title: Erythroid cells fixed with 0.5% formaldehyde replicate 2

description:
3C library preparation followed by double oligonucleotide capture
fixation_alpha.gfc
fixation_beta.gfc
fixation_slc25a37.gfc
05P2_S7_L001


title: Adult basal cell 13


title: Adult basal cell 14


title: Erythroid cells fixed with 1% formaldehyde replicate 1

description:
3C library preparation followed by double oligonucleotide capture
fixation_alpha.gfc
fixation_beta.gfc
fixation_slc25a37.gfc
1P1_S2_L001


title: Adult basal cell 12


title: Drosophila willistoni head small RNA [V119_dwil_head]

description: heads

source_name: D. willistoni head small RNA


title: Erythroid cells fixed with 0% formaldehyde replicate 2

description:
3C library preparation followed by double oligonucleotide capture
fixation_alpha.gfc
fixation_beta.gfc
fixation_slc25a37.gfc
0P2_S8_L001


title: Adult basal cell 11


title: Drosophila willistoni embryo small RNA [V118_dwil_embryo]

description: mixed embryos

source_name: D. willistoni embryo small RNA


title: Adult basal cell 8


title: Adult basal cell 9


title: Adult basal cell 7


title: Drosophila willistoni male body small RNA [V117_dwil_male_body]

description: male bodies

source_name: D. willistoni male body small RNA


title: Adult basal cell 10


title: Erythroid cells fixed with 0% formaldehyde replicate 1

description:
3C library preparation followed by double oligonucleotide capture
fixation_alpha.gfc
fixation_beta.gfc
fixation_slc25a37.gfc
0P1_S4_L001

source_name: Primary erythroid cells