title: Mouse Rbp4+ PFC/OFC cells 1000701602_H2__N337Barcode_715-517_S180


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L22_S159

status: Public on Nov 21 2020

type: SRA

city: Stanford

first: Justus

middle: M

last: Kebschull

state: CA

address: 327 Campus Drive

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Basecalling through Illumina pipeline
STAR alignment to (I) mouse genome mm10
Count reads in exons using Htseq
Produce count matrix
Analyse in Seurat
Genome_build: mm10
Supplementary_files_format_and_content: seurat v3 object containing count matrix, dimensionality reduction, cluster assignment, metadata

molecule: total RNA

organism: Mus musculus

source_name: medial prefrontal cortex

extract_protocol:
mPFC or OFC was dissected form acute slices of the mouse brain. Samples were digested and cells released by tirturation. TdTomato+ cells were FACS sorted into 384 well plates
smartseq2

tag: genotype


title: Mouse Rbp4+ PFC/OFC cells 1000701602_G1__N337Barcode_728-506_S167


title: 298s_G16

city: Huddinge

first: Ping

last: Chen

address: Alfred Nobels allé 8

department: Department of Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: mouse_glom_single_cell_unbiased_rpkms.txt

data_processing:
Raw sequencing data were de-multiplexed and converted into fastq format for each cell by using Illumina bcl2fastq with default setting.
Reads from mouse and human data were aligned to mouse genome mm10 and human genome hg38, respectively, using the STAR aligner.
Uniquely aligned reads mapping to the RefSeq gene annotations were used for gene expression estimates at reads per kilobase transcript and million mapped reads (RPKMs) using rpkmforgenes.
Low quality cells were excluded from downstream analysis when they failed to meet the following criteria for retaining cells: 1) >= 50,000 sequence reads; 2) >= 40% of reads uniquely aligned to the genome; 3) >= 40% of these reads mapping to RefSeq annotated exons; 4) < 10% of uniquely mapped reads from ERCC spike-ins; and 5) >= 500 genes with RPKM >= 1. In addition, doublets detected by Scrublet were further removed.
Genome_build: mm10 for mouse; hg38 for human
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each single cell

source_name: Kidney glomerular single cells - mouse kidney glomeruli (unbiased sorting)

extract_protocol:
Single cell preparation consisted of two main procedures: (1) Isolation of the glomerulus: mice were first perfused with Dynabeads via heart; minced fresh human healthy biopies and mouse kidney were incubated with Collagenase IV (1mg/ml) and DNase I (50U/ml) at 37°C for 15 and 30 min, respectively. Human samples then were sieved once through 300µm-strainers and isolated glomeruli collected via 100µm-strainers. Mouse samples went through 100µm-strainers twice and bead-containing glomeruli were separated from tubules via a magnet holder followed by 3x wash. (2) Single cell dissociation: isolated human or mouse glomeruli were digested with 1x PBS with Ca++/Mg++ containing collagenase IV (1mg/ml), pronase (1mg/ml) and DNaseI (50U/ml) at 37°C for 15 min with mild shaking (400rpm). Dissociated cells were washed once. For sorting viable single cells, a live cell dye (CMFDA-Green or DRAQ5) was used.
The reverse-transcribed cDNA from single cells was amplified 23 cycles followed by tagmentation and a standard index PCR. The single cell libraries were prepared according to Smart-seq2 protocol. The sequencing was performed on HISEQ 3000 (IIlumina).

tag: tissue

value: Kidney glomerulus

tag: strain

tag: cell sorting strategy

value: unbiased all viable cell sorting


title: Mouse Rbp4+ PFC/OFC cells 1000701602_F9__N337Barcode_723-506_S163


title: Mouse Rbp4+ PFC/OFC cells 1000701602_G12__N337Barcode_712-517_S178


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L23_S160


title: 294s_P20


title: Mouse Rbp4+ PFC/OFC cells 1000701602_G11__N337Barcode_711-517_S177


title: 294s_P18


title: Mouse Rbp4+ PFC/OFC cells 1000701602_F8__N337Barcode_722-506_S162


title: Mouse Rbp4+ PFC/OFC cells 1000701602_G10__N337Barcode_710-517_S176


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L21_S158


title: Mouse Rbp4+ PFC/OFC cells 1000701602_F7__N337Barcode_721-506_S161


title: 298s_K5


title: Mouse Rbp4+ PFC/OFC cells 1000701602_G5__N337Barcode_703-517_S171


title: 812s_J21


title: Mouse Rbp4+ PFC/OFC cells 1000701602_F6__N337Barcode_720-506_S160


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L20_S157


title: Mouse Rbp4+ PFC/OFC cells 1000701602_F5__N337Barcode_719-506_S159


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L1_S138


title: 121s_N23


title: 812s_I9


title: Mouse Rbp4+ PFC/OFC cells 1000701602_F4__N337Barcode_718-506_S158


title: Mouse Rbp4+ PFC/OFC cells 1000701602_F12__N337Barcode_727-506_S166


title: 682s_F19


title: Mouse Rbp4+ PFC/OFC cells 1000701602_F2__N337Barcode_715-506_S156


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L18_S155


title: Mouse Rbp4+ PFC/OFC cells 1000701602_F3__N337Barcode_716-506_S157


title: Mouse Rbp4+ PFC/OFC cells 1000701602_F1__N337Barcode_714-506_S155


title: Mouse Rbp4+ PFC/OFC cells 1000701602_F11__N337Barcode_726-506_S165


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L19_S156


title: Mouse Rbp4+ PFC/OFC cells 1000701602_F10__N337Barcode_724-506_S164


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L16_S153


title: Mouse Rbp4+ PFC/OFC cells 1000701602_E9__N337Barcode_707-506_S151


title: Mouse Rbp4+ PFC/OFC cells 1000701602_E8__N337Barcode_706-506_S150


title: 294s_K1


title: 812s_H6


title: Mouse Rbp4+ PFC/OFC cells 1000701602_E7__N337Barcode_705-506_S149


title: Mouse Rbp4+ PFC/OFC cells 1000701602_E6__N337Barcode_704-506_S148


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L15_S152


title: Mouse Rbp4+ PFC/OFC cells 1000701602_E4__N337Barcode_702-506_S146


title: Mouse Rbp4+ PFC/OFC cells 1000701602_E5__N337Barcode_703-506_S147


title: 682s_K19


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L13_S150


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L14_S151


title: Mouse Rbp4+ PFC/OFC cells 1000701602_E3__N337Barcode_701-506_S145


title: 812s_N16


title: Mouse Rbp4+ PFC/OFC cells 1000701602_E2__N337Barcode_729-516_S144


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L12_S149


title: 811s_G19


title: Mouse Rbp4+ PFC/OFC cells 1000701602_E12__N337Barcode_712-506_S154


title: 811s_B20


title: Mouse Rbp4+ PFC/OFC cells 1000701602_E1__N337Barcode_728-516_S143


title: Mouse Rbp4+ PFC/OFC cells 1000701602_D9__N337Barcode_723-516_S139


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L11_S148


title: Mouse Rbp4+ PFC/OFC cells 1000701602_E11__N337Barcode_711-506_S153


title: Mouse Rbp4+ PFC/OFC cells LLJL10_L10_S147


title: 299s_D20


title: Mouse Rbp4+ PFC/OFC cells 1000701602_E10__N337Barcode_710-506_S152


title: Mouse Rbp4+ PFC/OFC cells 1000701602_D8__N337Barcode_722-516_S138


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K9_S123


title: 121s_L19


title: 813s_C1


title: Mouse Rbp4+ PFC/OFC cells 1000701602_D4__N337Barcode_718-516_S134


title: Mouse Rbp4+ PFC/OFC cells 1000701602_D6__N337Barcode_720-516_S136


title: Mouse Rbp4+ PFC/OFC cells 1000701602_D5__N337Barcode_719-516_S135


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K8_S122


title: Mouse Rbp4+ PFC/OFC cells 1000701602_D3__N337Barcode_716-516_S133


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K6_S120


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K7_S121


title: Mouse Rbp4+ PFC/OFC cells 1000701602_D1__N337Barcode_714-516_S131


title: Mouse Rbp4+ PFC/OFC cells 1000701602_D2__N337Barcode_715-516_S132


title: 682s_E11


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K5_S119


title: 298s_E19


title: Mouse Rbp4+ PFC/OFC cells 1000701602_D12__N337Barcode_727-516_S142


title: Mouse Rbp4+ PFC/OFC cells 1000701602_D11__N337Barcode_726-516_S141


title: Mouse Rbp4+ PFC/OFC cells 1000701602_C9__N337Barcode_707-516_S127


title: Mouse Rbp4+ PFC/OFC cells 1000701602_D10__N337Barcode_724-516_S140


title: 811s_J1


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K3_S117


title: Mouse Rbp4+ PFC/OFC cells 1000701602_C7__N337Barcode_705-516_S125


title: Mouse Rbp4+ PFC/OFC cells 1000701602_C8__N337Barcode_706-516_S126


title: 298s_M18


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K4_S118


title: Mouse Rbp4+ PFC/OFC cells 1000701602_C5__N337Barcode_703-516_S123


title: Mouse Rbp4+ PFC/OFC cells 1000701602_C6__N337Barcode_704-516_S124


title: 294s_E12


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K2_S116


title: 812s_G9


title: Mouse Rbp4+ PFC/OFC cells 1000701602_D7__N337Barcode_721-516_S137


title: Mouse Rbp4+ PFC/OFC cells 1000701602_C3__N337Barcode_701-516_S121


title: Mouse Rbp4+ PFC/OFC cells 1000701602_C4__N337Barcode_702-516_S122


title: Mouse Rbp4+ PFC/OFC cells 1000701602_C1__N337Barcode_728-505_S119


title: Mouse Rbp4+ PFC/OFC cells 1000701602_C11__N337Barcode_711-516_S129


title: 298s_J8


title: 299s_A5


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K22_S136


title: 682s_N14


title: Mouse Rbp4+ PFC/OFC cells 1000701602_C2__N337Barcode_729-505_S120


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K21_S135


title: 555s_E11


title: Mouse Rbp4+ PFC/OFC cells 1000701602_C12__N337Barcode_712-516_S130


title: Mouse Rbp4+ PFC/OFC cells 1000701602_C10__N337Barcode_710-516_S128


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K20_S134


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K1_S115


title: Mouse Rbp4+ PFC/OFC cells 1000701602_B9__N337Barcode_723-505_S115


title: Mouse Rbp4+ PFC/OFC cells 1000701602_B7__N337Barcode_721-505_S113


title: 294s_I7


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K19_S133


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K18_S132


title: Mouse Rbp4+ PFC/OFC cells 1000701602_B5__N337Barcode_719-505_S111


title: 294s_E10


title: Mouse Rbp4+ PFC/OFC cells 1000701602_B6__N337Barcode_720-505_S112


title: Mouse Rbp4+ PFC/OFC cells 1000701602_B4__N337Barcode_718-505_S110


title: 294s_M19


title: 196s_L12


title: 121s_B4


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K16_S130


title: Mouse Rbp4+ PFC/OFC cells 1000701602_B3__N337Barcode_716-505_S109


title: 294s_P4


title: Mouse Rbp4+ PFC/OFC cells 1000701602_B8__N337Barcode_722-505_S114


title: Mouse Rbp4+ PFC/OFC cells 1000701602_A8__N337Barcode_706-505_S102


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K17_S131


title: Mouse Rbp4+ PFC/OFC cells 1000701602_B11__N337Barcode_726-505_S117


title: 682s_G7


title: Mouse Rbp4+ PFC/OFC cells 1000701602_B2__N337Barcode_715-505_S108


title: Mouse Rbp4+ PFC/OFC cells 1000701602_B10__N337Barcode_724-505_S116


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K15_S129


title: Mouse Rbp4+ PFC/OFC cells 1000701602_B12__N337Barcode_727-505_S118


title: 294s_O11


title: Mouse Rbp4+ PFC/OFC cells 1000701602_A9__N337Barcode_707-505_S103


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K12_S126


title: Mouse Rbp4+ PFC/OFC cells 1000701602_B1__N337Barcode_714-505_S107


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K14_S128


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K13_S127


title: Mouse Rbp4+ PFC/OFC cells 1000701602_A7__N337Barcode_705-505_S101


title: Mouse Rbp4+ PFC/OFC cells 1000701602_A5__N337Barcode_703-505_S99


title: 812s_D22


title: Mouse Rbp4+ PFC/OFC cells 1000701602_A4__N337Barcode_702-505_S98


title: 814s_G5


title: Mouse Rbp4+ PFC/OFC cells 1000701602_A6__N337Barcode_704-505_S100


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K11_S125


title: Mouse Rbp4+ PFC/OFC cells LLJL10_K10_S124


title: 813s_M15


title: Mouse Rbp4+ PFC/OFC cells 1000701602_A2__N337Barcode_729-515_S96


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J9_S100


title: Mouse Rbp4+ PFC/OFC cells 1000701602_A11__N337Barcode_711-505_S105


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J7_S98


title: Mouse Rbp4+ PFC/OFC cells 1000701602_A10__N337Barcode_710-505_S104


title: 121s_E20


title: Mouse Rbp4+ PFC/OFC cells 1000701602_A12__N337Barcode_712-505_S106


title: Mouse Rbp4+ PFC/OFC cells 1000701601_H9__N337Barcode_723-515_S91


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J6_S97


title: Mouse Rbp4+ PFC/OFC cells 1000701601_H8__N337Barcode_722-515_S90


title: Mouse Rbp4+ PFC/OFC cells 1000701601_H7__N337Barcode_721-515_S89


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J5_S96


title: Mouse Rbp4+ PFC/OFC cells 1000701601_H6__N337Barcode_720-515_S88


title: Mouse Rbp4+ PFC/OFC cells 1000701601_H2__N337Barcode_716-515_S85


title: 298s_I11


title: Mouse Rbp4+ PFC/OFC cells 1000701601_H3__N337Barcode_718-515_S86


title: Mouse Rbp4+ PFC/OFC cells 1000701601_H1__N337Barcode_715-515_S84


title: Mouse Rbp4+ PFC/OFC cells 1000701602_A3__N337Barcode_701-505_S97


title: Mouse Rbp4+ PFC/OFC cells 1000701601_H11__N337Barcode_726-515_S93


title: Mouse Rbp4+ PFC/OFC cells 1000701601_H12__N337Barcode_727-515_S94


title: Mouse Rbp4+ PFC/OFC cells 1000701602_A1__N337Barcode_728-515_S95


title: 294s_C14


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J4_S95


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J2_S93


title: 196s_M5


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J3_S94


title: 294s_D3


title: Mouse Rbp4+ PFC/OFC cells 1000701601_H10__N337Barcode_724-515_S92


title: 121s_E1


title: Mouse Rbp4+ PFC/OFC cells 1000701601_G9__N337Barcode_710-515_S80


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J23_S114


title: Mouse Rbp4+ PFC/OFC cells 1000701601_H5__N337Barcode_719-515_S87


title: 298s_E5


title: Mouse Rbp4+ PFC/OFC cells 1000701601_G8__N337Barcode_707-515_S79


title: Mouse Rbp4+ PFC/OFC cells 1000701601_G7__N337Barcode_706-515_S78


title: Mouse Rbp4+ PFC/OFC cells 1000701601_G6__N337Barcode_705-515_S77


title: 814s_D3


title: Mouse Rbp4+ PFC/OFC cells 1000701601_G4__N337Barcode_703-515_S75


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J21_S112


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J1_S92


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J22_S113


title: Mouse Rbp4+ PFC/OFC cells 1000701601_G5__N337Barcode_704-515_S76


title: Mouse Rbp4+ PFC/OFC cells 1000701601_G1__N337Barcode_729-503_S72


title: Mouse Rbp4+ PFC/OFC cells 1000701601_G3__N337Barcode_702-515_S74


title: 813s_O21


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J19_S110


title: 299s_B7


title: Mouse Rbp4+ PFC/OFC cells 1000701601_G12__N337Barcode_714-515_S83


title: Mouse Rbp4+ PFC/OFC cells 1000701601_G11__N337Barcode_712-515_S82


title: 196s_O20


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J17_S108


title: 298s_E8


title: Mouse Rbp4+ PFC/OFC cells 1000701601_F9__N337Barcode_724-503_S68


title: Mouse Rbp4+ PFC/OFC cells 1000701601_F8__N337Barcode_723-503_S67


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J16_S107


title: 196s_K21


title: 121s_G18


title: Mouse Rbp4+ PFC/OFC cells 1000701601_F5__N337Barcode_720-503_S64


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J15_S106


title: Mouse Rbp4+ PFC/OFC cells 1000701601_G2__N337Barcode_701-515_S73


title: Mouse Rbp4+ PFC/OFC cells 1000701601_F6__N337Barcode_721-503_S65


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J14_S105


title: Mouse Rbp4+ PFC/OFC cells 1000701601_F4__N337Barcode_719-503_S63


title: Mouse Rbp4+ PFC/OFC cells 1000701601_F1__N337Barcode_715-503_S60


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J13_S104


title: Mouse Rbp4+ PFC/OFC cells 1000701601_F11__N337Barcode_727-503_S70


title: Mouse Rbp4+ PFC/OFC cells 1000701601_F12__N337Barcode_728-503_S71


title: 813s_C22


title: 811s_O17


title: 814s_E5


title: 294s_J24


title: Mouse Rbp4+ PFC/OFC cells 1000701601_F3__N337Barcode_718-503_S62


title: Mouse Rbp4+ PFC/OFC cells 1000701601_G10__N337Barcode_711-515_S81


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J18_S109


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J12_S103


title: Mouse Rbp4+ PFC/OFC cells 1000701601_F10__N337Barcode_726-503_S69


title: 813s_C7


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J11_S102


title: Mouse Rbp4+ PFC/OFC cells 1000701601_E9__N337Barcode_710-503_S56


title: Mouse Rbp4+ PFC/OFC cells 1000701601_F7__N337Barcode_722-503_S66


title: Mouse Rbp4+ PFC/OFC cells 1000701601_E8__N337Barcode_707-503_S55


title: Mouse Rbp4+ PFC/OFC cells 1000701601_E7__N337Barcode_706-503_S54


title: Mouse Rbp4+ PFC/OFC cells 1000701601_E6__N337Barcode_705-503_S53


title: 812s_K23


title: Mouse Rbp4+ PFC/OFC cells 1000701601_E4__N337Barcode_703-503_S51


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I9_S77


title: 298s_E12


title: Mouse Rbp4+ PFC/OFC cells LLJL10_J10_S101


title: Mouse Rbp4+ PFC/OFC cells 1000701601_F2__N337Barcode_716-503_S61


title: Mouse Rbp4+ PFC/OFC cells 1000701601_E5__N337Barcode_704-503_S52


title: 814s_H7


title: Mouse Rbp4+ PFC/OFC cells 1000701601_E3__N337Barcode_702-503_S50


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I8_S76


title: Mouse Rbp4+ PFC/OFC cells 1000701601_E1__N337Barcode_729-513_S48


title: 814s_C11


title: Mouse Rbp4+ PFC/OFC cells 1000701601_E11__N337Barcode_712-503_S58


title: Mouse Rbp4+ PFC/OFC cells 1000701601_E2__N337Barcode_701-503_S49


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I7_S75


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I6_S74


title: Mouse Rbp4+ PFC/OFC cells 1000701601_D9__N337Barcode_724-513_S44


title: Mouse Rbp4+ PFC/OFC cells 1000701601_E10__N337Barcode_711-503_S57


title: 812s_F1


title: Mouse Rbp4+ PFC/OFC cells 1000701601_D7__N337Barcode_722-513_S42


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I5_S73


title: 811s_B1


title: 299s_M22


title: Mouse Rbp4+ PFC/OFC cells 1000701601_D6__N337Barcode_721-513_S41


title: 813s_E1


title: Mouse Rbp4+ PFC/OFC cells 1000701601_D5__N337Barcode_720-513_S40


title: 555s_J10


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I2_S70


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I3_S71


title: Mouse Rbp4+ PFC/OFC cells 1000701601_D3__N337Barcode_718-513_S38


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I23_S91


title: 811s_A21


title: Mouse Rbp4+ PFC/OFC cells 1000701601_E12__N337Barcode_714-503_S59


title: Mouse Rbp4+ PFC/OFC cells 1000701601_D10__N337Barcode_726-513_S45


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I22_S90


title: Mouse Rbp4+ PFC/OFC cells 1000701601_D4__N337Barcode_719-513_S39


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I4_S72


title: Mouse Rbp4+ PFC/OFC cells 1000701601_D8__N337Barcode_723-513_S43


title: 294s_C6


title: Mouse Rbp4+ PFC/OFC cells 1000701601_C8__N337Barcode_707-513_S31


title: Mouse Rbp4+ PFC/OFC cells 1000701601_C9__N337Barcode_710-513_S32


title: Mouse Rbp4+ PFC/OFC cells 1000701601_D1__N337Barcode_715-513_S36


title: 812s_K11


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I21_S89


title: Mouse Rbp4+ PFC/OFC cells 1000701601_C7__N337Barcode_706-513_S30


title: Mouse Rbp4+ PFC/OFC cells 1000701601_D2__N337Barcode_716-513_S37


title: 121s_C15


title: Mouse Rbp4+ PFC/OFC cells 1000701601_C6__N337Barcode_705-513_S29


title: Mouse Rbp4+ PFC/OFC cells 1000701601_C5__N337Barcode_704-513_S28


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I1_S69


title: Mouse Rbp4+ PFC/OFC cells 1000701601_C4__N337Barcode_703-513_S27


title: 121s_D11


title: Mouse Rbp4+ PFC/OFC cells 1000701601_D12__N337Barcode_728-513_S47


title: Mouse Rbp4+ PFC/OFC cells 1000701601_C3__N337Barcode_702-513_S26


title: 294s_D22


title: Mouse Rbp4+ PFC/OFC cells 1000701601_C2__N337Barcode_701-513_S25


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I18_S86


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I19_S87


title: Mouse Rbp4+ PFC/OFC cells 1000701601_C12__N337Barcode_714-513_S35


title: Mouse Rbp4+ PFC/OFC cells 1000701601_C1__N337Barcode_729-502_S24


title: Mouse Rbp4+ PFC/OFC cells 1000701601_D11__N337Barcode_727-513_S46


title: Mouse Rbp4+ PFC/OFC cells 1000701601_C11__N337Barcode_712-513_S34


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I17_S85


title: 811s_C12


title: 812s_F13


title: Mouse Rbp4+ PFC/OFC cells 1000701601_B9__N337Barcode_724-502_S20


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I16_S84


title: Mouse Rbp4+ PFC/OFC cells 1000701601_B8__N337Barcode_723-502_S19


title: Mouse Rbp4+ PFC/OFC cells 1000701601_C10__N337Barcode_711-513_S33


title: Mouse Rbp4+ PFC/OFC cells 1000701601_B6__N337Barcode_721-502_S17


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I20_S88


title: 682s_A4


title: 294s_L7


title: Mouse Rbp4+ PFC/OFC cells 1000701601_B7__N337Barcode_722-502_S18


title: Mouse Rbp4+ PFC/OFC cells 1000701601_B5__N337Barcode_720-502_S16


title: Mouse Rbp4+ PFC/OFC cells 1000701601_B4__N337Barcode_719-502_S15


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I15_S83


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I14_S82


title: 682s_I5


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I13_S81


title: 196s_J21


title: 813s_A18


title: 813s_I22


title: Mouse Rbp4+ PFC/OFC cells 1000701601_B12__N337Barcode_728-502_S23


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I12_S80


title: Mouse Rbp4+ PFC/OFC cells 1000701601_B3__N337Barcode_718-502_S14


title: Mouse Rbp4+ PFC/OFC cells 1000701601_B2__N337Barcode_716-502_S13


title: Mouse Rbp4+ PFC/OFC cells 1000701601_B1__N337Barcode_715-502_S12


title: Mouse Rbp4+ PFC/OFC cells 1000701601_B11__N337Barcode_727-502_S22


title: Mouse Rbp4+ PFC/OFC cells 1000701601_B10__N337Barcode_726-502_S21


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I11_S79


title: Mouse Rbp4+ PFC/OFC cells 1000701601_A9__N337Barcode_711-502_S9


title: Mouse Rbp4+ PFC/OFC cells LLJL10_I10_S78


title: Mouse Rbp4+ PFC/OFC cells 1000701601_A7__N337Barcode_707-502_S7


title: Mouse Rbp4+ PFC/OFC cells 1000701601_A8__N337Barcode_710-502_S8


title: Mouse Rbp4+ PFC/OFC cells 1000701601_A6__N337Barcode_706-502_S6


title: 121s_O9


title: Mouse Rbp4+ PFC/OFC cells 1000701601_A5__N337Barcode_705-502_S5


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H8_S53


title: 294s_H21


title: Mouse Rbp4+ PFC/OFC cells 1000701601_A4__N337Barcode_704-502_S4


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H7_S52


title: 299s_H16


title: 682s_G15


title: Mouse Rbp4+ PFC/OFC cells 1000701601_A3__N337Barcode_703-502_S3


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H6_S51


title: Mouse Rbp4+ PFC/OFC cells 1000701601_A1__N337Barcode_701-502_S1


title: Mouse Rbp4+ PFC/OFC cells 1000701601_A10__N337Barcode_712-502_S10


title: Mouse Rbp4+ PFC/OFC cells 1000701601_A11__N337Barcode_714-502_S11


title: 298s_K1


title: 121s_C20


title: Mouse Rbp4+ PFC/OFC cells 1000701405_E7__N281BARCODE_707-520_S271


title: Mouse Rbp4+ PFC/OFC cells 1000701405_E8__N281BARCODE_710-520_S272


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H4_S49


title: Mouse Rbp4+ PFC/OFC cells 1000701405_E6__N281BARCODE_706-520_S270


title: Mouse Rbp4+ PFC/OFC cells 1000701405_E5__N281BARCODE_705-520_S269


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H9_S54


title: 813s_H3


title: Mouse Rbp4+ PFC/OFC cells 1000701405_E4__N281BARCODE_704-520_S268


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H5_S50


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H3_S48


title: 813s_B7


title: Mouse Rbp4+ PFC/OFC cells 1000701601_A2__N337Barcode_702-502_S2


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H2_S47


title: 813s_H11


title: Mouse Rbp4+ PFC/OFC cells 1000701405_E2__N281BARCODE_702-520_S266


title: Mouse Rbp4+ PFC/OFC cells 1000701405_D8__N281BARCODE_726-508_S261


title: Mouse Rbp4+ PFC/OFC cells 1000701405_E1__N281BARCODE_701-520_S265


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H23_S68


title: 298s_G19


title: Mouse Rbp4+ PFC/OFC cells 1000701405_E3__N281BARCODE_703-520_S267


title: Mouse Rbp4+ PFC/OFC cells 1000701405_D6__N281BARCODE_724-508_S260


title: 121s_F12


title: 812s_D3


title: Mouse Rbp4+ PFC/OFC cells 1000701405_D2__N281BARCODE_721-508_S257


title: 196s_L2


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H22_S67


title: Mouse Rbp4+ PFC/OFC cells 1000701405_D5__N281BARCODE_723-508_S259


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H21_S66


title: Mouse Rbp4+ PFC/OFC cells 1000701405_D10__N281BARCODE_727-508_S262


title: 299s_F4


title: Mouse Rbp4+ PFC/OFC cells 1000701405_D4__N281BARCODE_722-508_S258


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H20_S65


title: Mouse Rbp4+ PFC/OFC cells 1000701405_D12__N281BARCODE_729-508_S264


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H1_S46


title: 555s_G10


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H19_S64


title: Mouse Rbp4+ PFC/OFC cells 1000701404_H9__N281BARCODE_703-518_S219


title: Mouse Rbp4+ PFC/OFC cells 1000701404_H8__N281BARCODE_702-518_S218


title: Mouse Rbp4+ PFC/OFC cells 1000701404_H5__N281BARCODE_729-507_S216


title: 814s_H6


title: Mouse Rbp4+ PFC/OFC cells 1000701404_H3__N281BARCODE_727-507_S214


title: 299s_C13


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H18_S63


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H17_S62


title: Mouse Rbp4+ PFC/OFC cells 1000701404_H2__N281BARCODE_726-507_S213


title: Mouse Rbp4+ PFC/OFC cells 1000701404_H1__N281BARCODE_724-507_S212


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H16_S61


title: Mouse Rbp4+ PFC/OFC cells 1000701404_G9__N281BARCODE_720-507_S208


title: Mouse Rbp4+ PFC/OFC cells 1000701404_G7__N281BARCODE_719-507_S207


title: Mouse Rbp4+ PFC/OFC cells 1000701404_H11__N281BARCODE_704-518_S220


title: 298s_G14


title: Mouse Rbp4+ PFC/OFC cells 1000701404_H4__N281BARCODE_728-507_S215


title: Mouse Rbp4+ PFC/OFC cells 1000701404_G5__N281BARCODE_716-507_S205


title: Mouse Rbp4+ PFC/OFC cells 1000701404_G4__N281BARCODE_715-507_S204


title: 298s_M7


title: Mouse Rbp4+ PFC/OFC cells 1000701404_G6__N281BARCODE_718-507_S206


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H15_S60


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H13_S58


title: 812s_E1


title: 294s_F8


title: Mouse Rbp4+ PFC/OFC cells 1000701404_G2__N281BARCODE_712-507_S202


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H12_S57


title: Mouse Rbp4+ PFC/OFC cells 1000701404_G3__N281BARCODE_714-507_S203


title: Mouse Rbp4+ PFC/OFC cells 1000701404_G12__N281BARCODE_723-507_S211


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H14_S59


title: Mouse Rbp4+ PFC/OFC cells 1000701404_G10__N281BARCODE_721-507_S209


title: 555s_F5


title: Mouse Rbp4+ PFC/OFC cells 1000701404_G1__N281BARCODE_711-507_S201


title: 299s_D13


title: Mouse Rbp4+ PFC/OFC cells 1000701404_F9__N281BARCODE_705-507_S197


title: Mouse Rbp4+ PFC/OFC cells 1000701404_G11__N281BARCODE_722-507_S210


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H11_S56


title: Mouse Rbp4+ PFC/OFC cells LLJL10_H10_S55


title: Mouse Rbp4+ PFC/OFC cells 1000701404_F8__N281BARCODE_704-507_S196


title: Mouse Rbp4+ PFC/OFC cells 1000701404_F5__N281BARCODE_701-507_S193


title: 682s_G8


title: Mouse Rbp4+ PFC/OFC cells 1000701404_F6__N281BARCODE_702-507_S194


title: 294s_D18


title: Mouse Rbp4+ PFC/OFC cells 1000701404_F3__N281BARCODE_729-517_S192


title: 811s_G14


title: Mouse Rbp4+ PFC/OFC cells 1000701404_F2__N281BARCODE_728-517_S191


title: Mouse Rbp4+ PFC/OFC cells 1000701404_F1__N281BARCODE_727-517_S190


title: 298s_I5


title: Mouse Rbp4+ PFC/OFC cells 1000701404_F10__N281BARCODE_706-507_S198


title: Mouse Rbp4+ PFC/OFC cells 1000701404_F11__N281BARCODE_707-507_S199


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G7_S29


title: Mouse Rbp4+ PFC/OFC cells 1000701404_F12__N281BARCODE_710-507_S200


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G5_S27


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G6_S28


title: Mouse Rbp4+ PFC/OFC cells 1000701404_E9__N281BARCODE_723-517_S187


title: 299s_P18


title: Mouse Rbp4+ PFC/OFC cells 1000701404_F7__N281BARCODE_703-507_S195


title: 298s_G9


title: 294s_O6


title: Mouse Rbp4+ PFC/OFC cells 1000701404_E8__N281BARCODE_722-517_S186


title: Mouse Rbp4+ PFC/OFC cells 1000701404_E7__N281BARCODE_721-517_S185


title: 813s_K16


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G9_S31


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G4_S26


title: Mouse Rbp4+ PFC/OFC cells 1000701404_E6__N281BARCODE_720-517_S184


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G8_S30


title: Mouse Rbp4+ PFC/OFC cells 1000701404_E4__N281BARCODE_719-517_S183


title: Mouse Rbp4+ PFC/OFC cells 1000701404_E3__N281BARCODE_718-517_S182


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G3_S25


title: Mouse Rbp4+ PFC/OFC cells 1000701404_E1__N281BARCODE_716-517_S181


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G2_S24


title: Mouse Rbp4+ PFC/OFC cells 1000701404_E12__N281BARCODE_726-517_S189


title: 813s_K19


title: 294s_P5


title: Mouse Rbp4+ PFC/OFC cells 1000701404_E10__N281BARCODE_724-517_S188


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G23_S45


title: Mouse Rbp4+ PFC/OFC cells 1000701404_D9__N281BARCODE_712-517_S178


title: 811s_C13


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G22_S44


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G21_S43


title: Mouse Rbp4+ PFC/OFC cells 1000701404_D7__N281BARCODE_710-517_S176


title: Mouse Rbp4+ PFC/OFC cells 1000701404_D8__N281BARCODE_711-517_S177


title: 813s_N1


title: Mouse Rbp4+ PFC/OFC cells 1000701404_D5__N281BARCODE_706-517_S174


title: Mouse Rbp4+ PFC/OFC cells 1000701404_D2__N281BARCODE_703-517_S171


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G20_S42


title: Mouse Rbp4+ PFC/OFC cells 1000701404_D4__N281BARCODE_705-517_S173


title: 555s_P3


title: 682s_C15


title: Mouse Rbp4+ PFC/OFC cells 1000701404_D3__N281BARCODE_704-517_S172


title: Mouse Rbp4+ PFC/OFC cells 1000701404_D12__N281BARCODE_715-517_S180


title: Mouse Rbp4+ PFC/OFC cells 1000701404_D11__N281BARCODE_714-517_S179


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G19_S41


title: 811s_B4


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G1_S23


title: Mouse Rbp4+ PFC/OFC cells 1000701404_C7__N281BARCODE_728-506_S167


title: Mouse Rbp4+ PFC/OFC cells 1000701404_C6__N281BARCODE_727-506_S166


title: Mouse Rbp4+ PFC/OFC cells 1000701404_C5__N281BARCODE_726-506_S165


title: 294s_H9


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G17_S39


title: 294s_L5


title: Mouse Rbp4+ PFC/OFC cells 1000701404_C2__N281BARCODE_723-506_S163


title: Mouse Rbp4+ PFC/OFC cells 1000701404_C11__N281BARCODE_701-517_S169


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G16_S38


title: Mouse Rbp4+ PFC/OFC cells 1000701404_B9__N281BARCODE_719-506_S159


title: Mouse Rbp4+ PFC/OFC cells 1000701404_B8__N281BARCODE_718-506_S158


title: 813s_F24


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G15_S37


title: Mouse Rbp4+ PFC/OFC cells 1000701404_B6__N281BARCODE_715-506_S156


title: 814s_A12


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G14_S36


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G13_S35


title: Mouse Rbp4+ PFC/OFC cells 1000701404_B7__N281BARCODE_716-506_S157


title: Mouse Rbp4+ PFC/OFC cells 1000701404_C8__N281BARCODE_729-506_S168


title: Mouse Rbp4+ PFC/OFC cells 1000701404_B4__N281BARCODE_714-506_S155


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G12_S34


title: 682s_M20


title: 196s_N5


title: Mouse Rbp4+ PFC/OFC cells 1000701404_B3__N281BARCODE_712-506_S154


title: Mouse Rbp4+ PFC/OFC cells 1000701404_C3__N281BARCODE_724-506_S164


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G18_S40


title: Mouse Rbp4+ PFC/OFC cells 1000701404_B11__N281BARCODE_721-506_S161


title: 813s_H4


title: Mouse Rbp4+ PFC/OFC cells 1000701404_B12__N281BARCODE_722-506_S162


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G11_S33


title: 812s_M17


title: Mouse Rbp4+ PFC/OFC cells 1000701404_A9__N281BARCODE_705-506_S149


title: 294s_O1


title: Mouse Rbp4+ PFC/OFC cells 1000701404_B10__N281BARCODE_720-506_S160


title: Mouse Rbp4+ PFC/OFC cells 1000701404_A7__N281BARCODE_704-506_S148


title: Mouse Rbp4+ PFC/OFC cells LLJL10_G10_S32


title: 682s_F16


title: 682s_G1


title: Mouse Rbp4+ PFC/OFC cells 1000701404_B1__N281BARCODE_711-506_S153


title: Mouse Rbp4+ PFC/OFC cells 1000701404_A3__N281BARCODE_701-506_S145


title: Mouse Rbp4+ PFC/OFC cells 1000701404_A2__N281BARCODE_729-516_S144


title: Mouse Rbp4+ PFC/OFC cells 1000701404_A5__N281BARCODE_702-506_S146


title: Mouse Rbp4+ PFC/OFC cells 1000701404_A6__N281BARCODE_703-506_S147


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F8_S7


title: Mouse Rbp4+ PFC/OFC cells 1000701404_A12__N281BARCODE_710-506_S152


title: Mouse Rbp4+ PFC/OFC cells 1000701404_A10__N281BARCODE_706-506_S150


title: 294s_G16


title: 812s_N3


title: Mouse Rbp4+ PFC/OFC cells 1000701403_H7__N281BARCODE_723-516_S139


title: Mouse Rbp4+ PFC/OFC cells 1000701403_H9__N281BARCODE_726-516_S141


title: 555s_H11


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F7_S6


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F5_S4


title: Mouse Rbp4+ PFC/OFC cells 1000701403_H5__N281BARCODE_722-516_S138


title: Mouse Rbp4+ PFC/OFC cells 1000701403_H8__N281BARCODE_724-516_S140


title: 298s_C6


title: Mouse Rbp4+ PFC/OFC cells 1000701403_H3__N281BARCODE_720-516_S136


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F9_S8


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F4_S3


title: Mouse Rbp4+ PFC/OFC cells 1000701403_H4__N281BARCODE_721-516_S137


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F2_S1


title: 811s_E12


title: Mouse Rbp4+ PFC/OFC cells 1000701404_A11__N281BARCODE_707-506_S151


title: Mouse Rbp4+ PFC/OFC cells 1000701403_G9__N281BARCODE_715-516_S132


title: Mouse Rbp4+ PFC/OFC cells 1000701403_G5__N281BARCODE_714-516_S131


title: 299s_C12


title: Mouse Rbp4+ PFC/OFC cells 1000701403_G4__N281BARCODE_712-516_S130


title: 813s_I21


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F6_S5


title: Mouse Rbp4+ PFC/OFC cells 1000701403_G3__N281BARCODE_711-516_S129


title: Mouse Rbp4+ PFC/OFC cells 1000701403_G2__N281BARCODE_710-516_S128


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F22_S21


title: 298s_D1


title: Mouse Rbp4+ PFC/OFC cells 1000701403_G12__N281BARCODE_718-516_S134


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F21_S20


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F20_S19


title: Mouse Rbp4+ PFC/OFC cells 1000701403_G10__N281BARCODE_716-516_S133


title: Mouse Rbp4+ PFC/OFC cells 1000701403_G1__N281BARCODE_707-516_S127


title: 811s_L3


title: Mouse Rbp4+ PFC/OFC cells 1000701403_F7__N281BARCODE_705-516_S125


title: Mouse Rbp4+ PFC/OFC cells 1000701403_H1__N281BARCODE_719-516_S135


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F3_S2


title: Mouse Rbp4+ PFC/OFC cells 1000701403_F5__N281BARCODE_704-516_S124


title: 813s_I8


title: 814s_G17


title: Mouse Rbp4+ PFC/OFC cells 1000701403_F4__N281BARCODE_703-516_S123


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F23_S22


title: Mouse Rbp4+ PFC/OFC cells 1000701403_F3__N281BARCODE_702-516_S122


title: Mouse Rbp4+ PFC/OFC cells 1000701403_F2__N281BARCODE_701-516_S121


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F1_S300


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F19_S18


title: 813s_H16


title: 812s_I7


title: Mouse Rbp4+ PFC/OFC cells 1000701403_E8__N281BARCODE_723-505_S115


title: 121s_P5


title: Mouse Rbp4+ PFC/OFC cells 1000701403_F12__N281BARCODE_706-516_S126


title: Mouse Rbp4+ PFC/OFC cells 1000701403_E7__N281BARCODE_722-505_S114


title: Mouse Rbp4+ PFC/OFC cells 1000701403_E6__N281BARCODE_721-505_S113


title: 555s_C3


title: Mouse Rbp4+ PFC/OFC cells 1000701403_E1__N281BARCODE_718-505_S110


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F15_S14


title: Mouse Rbp4+ PFC/OFC cells 1000701403_E5__N281BARCODE_720-505_S112


title: 299s_B12


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F18_S17


title: 682s_G11


title: Mouse Rbp4+ PFC/OFC cells 1000701403_E11__N281BARCODE_727-505_S118


title: Mouse Rbp4+ PFC/OFC cells 1000701403_E3__N281BARCODE_719-505_S111


title: Mouse Rbp4+ PFC/OFC cells 1000701403_E12__N281BARCODE_728-505_S119


title: 298s_E15


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F14_S13


title: Mouse Rbp4+ PFC/OFC cells 1000701403_D8__N281BARCODE_715-505_S108


title: Mouse Rbp4+ PFC/OFC cells 1000701403_F1__N281BARCODE_729-505_S120


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F13_S12


title: Mouse Rbp4+ PFC/OFC cells 1000701403_H10__N281BARCODE_727-516_S142


title: Mouse Rbp4+ PFC/OFC cells 1000701403_D6__N281BARCODE_712-505_S106


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F12_S11


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F17_S16


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F16_S15


title: 294s_J19


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F11_S10


title: Mouse Rbp4+ PFC/OFC cells 1000701403_D5__N281BARCODE_711-505_S105


title: Mouse Rbp4+ PFC/OFC cells 1000701403_D4__N281BARCODE_710-505_S104


title: Mouse Rbp4+ PFC/OFC cells 1000701403_D2__N281BARCODE_706-505_S102


title: 813s_E18


title: Mouse Rbp4+ PFC/OFC cells LLJL10_F10_S9


title: Mouse Rbp4+ PFC/OFC cells 1000701403_D1__N281BARCODE_705-505_S101


title: Mouse Rbp4+ PFC/OFC cells 1000701403_E10__N281BARCODE_726-505_S117


title: Mouse Rbp4+ PFC/OFC cells 1000701403_C8__N281BARCODE_701-505_S97


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E9_S285


title: 299s_A2


title: 814s_H13


title: Mouse Rbp4+ PFC/OFC cells 1000701403_C7__N281BARCODE_729-515_S96


title: Mouse Rbp4+ PFC/OFC cells 1000701403_C5__N281BARCODE_728-515_S95


title: Mouse Rbp4+ PFC/OFC cells 1000701403_D7__N281BARCODE_714-505_S107


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E7_S283


title: Mouse Rbp4+ PFC/OFC cells 1000701403_C4__N281BARCODE_727-515_S94


title: 814s_D2


title: 812s_B3


title: Mouse Rbp4+ PFC/OFC cells 1000701403_C9__N281BARCODE_702-505_S98


title: 299s_B20


title: Mouse Rbp4+ PFC/OFC cells 1000701403_C1__N281BARCODE_726-515_S93


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E6_S282


title: Mouse Rbp4+ PFC/OFC cells 1000701403_C11__N281BARCODE_703-505_S99


title: 298s_M11


title: Mouse Rbp4+ PFC/OFC cells 1000701403_D3__N281BARCODE_707-505_S103


title: Mouse Rbp4+ PFC/OFC cells 1000701403_B9__N281BARCODE_723-515_S91


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E5_S281


title: Mouse Rbp4+ PFC/OFC cells 1000701403_B8__N281BARCODE_722-515_S90


title: 813s_H10


title: Mouse Rbp4+ PFC/OFC cells 1000701403_B5__N281BARCODE_720-515_S88


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E8_S284


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E4_S280


title: 299s_C20


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E3_S279


title: Mouse Rbp4+ PFC/OFC cells 1000701403_B4__N281BARCODE_719-515_S87


title: Mouse Rbp4+ PFC/OFC cells 1000701403_D11__N281BARCODE_716-505_S109


title: Mouse Rbp4+ PFC/OFC cells 1000701403_B1__N281BARCODE_715-515_S84


title: Mouse Rbp4+ PFC/OFC cells 1000701403_A9__N281BARCODE_712-515_S82


title: Mouse Rbp4+ PFC/OFC cells 1000701403_B2__N281BARCODE_716-515_S85


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E20_S296


title: Mouse Rbp4+ PFC/OFC cells 1000701403_A1__N281BARCODE_704-515_S76


title: Mouse Rbp4+ PFC/OFC cells 1000701403_B12__N281BARCODE_724-515_S92


title: 294s_L2


title: 294s_G17


title: 121s_O11


title: Mouse Rbp4+ PFC/OFC cells 1000701403_B3__N281BARCODE_718-515_S86


title: Mouse Rbp4+ PFC/OFC cells 1000701403_A4__N281BARCODE_706-515_S78


title: Mouse Rbp4+ PFC/OFC cells 1000701403_A5__N281BARCODE_707-515_S79


title: 555s_C9


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E23_S299


title: Mouse Rbp4+ PFC/OFC cells 1000701403_A12__N281BARCODE_714-515_S83


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E1_S277


title: Mouse Rbp4+ PFC/OFC cells 1000701403_A6__N281BARCODE_710-515_S80


title: Mouse Rbp4+ PFC/OFC cells 1000701101_H7__IL699-724-522_S380


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E19_S295


title: Mouse Rbp4+ PFC/OFC cells 1000701101_H9__IL699-727-522_S382


title: Mouse Rbp4+ PFC/OFC cells 1000701403_B7__N281BARCODE_721-515_S89


title: 812s_D23


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E18_S294


title: Mouse Rbp4+ PFC/OFC cells 1000701101_H5__IL699-723-522_S379


title: 813s_D9


title: 813s_B17


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E21_S297


title: Mouse Rbp4+ PFC/OFC cells 1000701101_H4__IL699-722-522_S378


title: Mouse Rbp4+ PFC/OFC cells 1000701101_H3__IL699-721-522_S377


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E17_S293


title: 294s_B10


title: Mouse Rbp4+ PFC/OFC cells 1000701101_H11__IL699-728-522_S383


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E15_S291


title: Mouse Rbp4+ PFC/OFC cells 1000701101_H12__IL699-729-522_S384


title: Mouse Rbp4+ PFC/OFC cells 1000701101_G8__IL699-716-522_S373


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E22_S298


title: 298s_G18


title: Mouse Rbp4+ PFC/OFC cells 1000701101_H8__IL699-726-522_S381


title: Mouse Rbp4+ PFC/OFC cells 1000701101_G4__IL699-715-522_S372


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E14_S290


title: Mouse Rbp4+ PFC/OFC cells 1000701101_G3__IL699-714-522_S371


title: Mouse Rbp4+ PFC/OFC cells 1000701101_G12__IL699-719-522_S375


title: 196s_L14


title: Mouse Rbp4+ PFC/OFC cells 1000701101_G10__IL699-718-522_S374


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E13_S289


title: Mouse Rbp4+ PFC/OFC cells 1000701101_F7__IL699-706-522_S366


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E12_S288


title: 121s_G15


title: Mouse Rbp4+ PFC/OFC cells 1000701101_F9__IL699-707-522_S367


title: Mouse Rbp4+ PFC/OFC cells 1000701101_G1__IL699-712-522_S370


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E11_S287


title: 298s_N14


title: Mouse Rbp4+ PFC/OFC cells 1000701101_F6__IL699-705-522_S365


title: Mouse Rbp4+ PFC/OFC cells 1000701101_F3__IL699-704-522_S364


title: Mouse Rbp4+ PFC/OFC cells LLJL10_E10_S286


title: Mouse Rbp4+ PFC/OFC cells 1000701101_F2__IL699-703-522_S363


title: 555s_P2


title: 811s_G10


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D9_S262


title: Mouse Rbp4+ PFC/OFC cells 1000701101_F10__IL699-710-522_S368


title: Mouse Rbp4+ PFC/OFC cells 1000701101_F1__IL699-702-522_S362


title: Mouse Rbp4+ PFC/OFC cells 1000701101_F12__IL699-711-522_S369


title: 814s_H20


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D8_S261


title: Mouse Rbp4+ PFC/OFC cells 1000701101_E8__IL699-727-511_S358


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D7_S260


title: 813s_K9


title: 299s_P16


title: 299s_N19


title: Mouse Rbp4+ PFC/OFC cells 1000701101_E9__IL699-728-511_S359


title: Mouse Rbp4+ PFC/OFC cells 1000701101_E7__IL699-726-511_S357


title: Mouse Rbp4+ PFC/OFC cells 1000701101_E4__IL699-723-511_S355


title: Mouse Rbp4+ PFC/OFC cells 1000701101_E12__IL699-701-522_S361


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D5_S258


title: Mouse Rbp4+ PFC/OFC cells 1000701101_E11__IL699-729-511_S360


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D6_S259


title: 299s_O21


title: 299s_J15


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D4_S257


title: Mouse Rbp4+ PFC/OFC cells 1000701101_D7__IL699-720-511_S352


title: Mouse Rbp4+ PFC/OFC cells 1000701101_D6__IL699-719-511_S351


title: Mouse Rbp4+ PFC/OFC cells 1000701101_D4__IL699-718-511_S350


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D3_S256


title: 812s_I21


title: 813s_A22


title: Mouse Rbp4+ PFC/OFC cells 1000701101_D3__IL699-716-511_S349


title: Mouse Rbp4+ PFC/OFC cells 1000701101_D1__IL699-714-511_S347


title: 298s_I21


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D2_S255


title: Mouse Rbp4+ PFC/OFC cells 1000701101_C9__IL699-712-511_S346


title: Mouse Rbp4+ PFC/OFC cells 1000701101_E5__IL699-724-511_S356


title: Mouse Rbp4+ PFC/OFC cells 1000701101_D11__IL699-722-511_S354


title: Mouse Rbp4+ PFC/OFC cells 1000701101_D10__IL699-721-511_S353


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D23_S276


title: 294s_N13


title: Mouse Rbp4+ PFC/OFC cells 1000701101_C5__IL699-710-511_S344


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D22_S275


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D21_S274


title: Mouse Rbp4+ PFC/OFC cells 1000701101_C4__IL699-707-511_S343


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D20_S273


title: Mouse Rbp4+ PFC/OFC cells 1000701101_B8__IL699-703-511_S339


title: 298s_J10


title: Mouse Rbp4+ PFC/OFC cells 1000701101_B7__IL699-702-511_S338


title: Mouse Rbp4+ PFC/OFC cells 1000701101_C6__IL699-711-511_S345


title: 813s_J10


title: Mouse Rbp4+ PFC/OFC cells 1000701101_C1__IL699-705-511_S341


title: 811s_G4


title: Mouse Rbp4+ PFC/OFC cells 1000701101_B4__IL699-729-521_S336


title: Mouse Rbp4+ PFC/OFC cells 1000701101_B6__IL699-701-511_S337


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D19_S272


title: 682s_K6


title: 812s_P17


title: Mouse Rbp4+ PFC/OFC cells 1000701101_B11__IL699-704-511_S340


title: Mouse Rbp4+ PFC/OFC cells 1000701101_B2__IL699-728-521_S335


title: 196s_M1


title: Mouse Rbp4+ PFC/OFC cells 1000701101_A3__IL699-727-521_S334


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D17_S270


title: Mouse Rbp4+ PFC/OFC cells 1000701101_A2__IL699-726-521_S333


title: 811s_F4


title: Mouse Rbp4+ PFC/OFC cells 1000700901_H7__IL699-724-518_S236


title: Mouse Rbp4+ PFC/OFC cells 1000701101_C3__IL699-706-511_S342


title: Mouse Rbp4+ PFC/OFC cells 1000700901_H9__IL699-726-518_S237


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D18_S271


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D16_S269


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D1_S254


title: 812s_K12


title: Mouse Rbp4+ PFC/OFC cells 1000700901_H4__IL699-721-518_S233


title: Mouse Rbp4+ PFC/OFC cells 1000700901_H6__IL699-723-518_S235


title: 299s_P20


title: Mouse Rbp4+ PFC/OFC cells 1000700901_H3__IL699-720-518_S232


title: Mouse Rbp4+ PFC/OFC cells 1000700901_H5__IL699-722-518_S234


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D14_S267


title: 121s_A24


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D15_S268


title: Mouse Rbp4+ PFC/OFC cells 1000700901_H12__IL699-727-518_S238


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D12_S265


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D13_S266


title: Mouse Rbp4+ PFC/OFC cells 1000700901_G9__IL699-716-518_S229


title: 299s_H23


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D11_S264


title: Mouse Rbp4+ PFC/OFC cells 1000700901_G7__IL699-715-518_S228


title: Mouse Rbp4+ PFC/OFC cells LLJL10_D10_S263


title: 682s_P3


title: 812s_J12


title: Mouse Rbp4+ PFC/OFC cells 1000700901_G6__IL699-714-518_S227


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C9_S239


title: 555s_A6


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C8_S238


title: 682s_M11


title: Mouse Rbp4+ PFC/OFC cells 1000700901_G4__IL699-712-518_S226


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C7_S237


title: Mouse Rbp4+ PFC/OFC cells 1000700901_G3__IL699-711-518_S225


title: 196s_M24


title: Δ4AQ strain grown in LB with HQNO, biological rep 1

type: RNA

city: Rome

first: Emanuela

last: Frangipani

address: Viale G. Marconi 446

department: Department of Sciences

country: Italy

institute: University of Roma Tre

description: cells grown to OD600 of 1.5

hyb_protocol: Following labeling, 1 ug of cDNA was hybridized for 16 hr at 50C on GeneChip P. aeruginosa Genome Array. GeneChips were washed and stained according to the protocol described in Affymetrix GeneChip Expression Analysis manual (Fluidics protocol FlexMidi_euk2v3_450).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Raw data were extracted from the scanned images. The RMA algorithm was applied to the data, using Affymetrix Expression Console software.

label: biotin

organism: Pseudomonas aeruginosa PAO1

source_name: P. aeruginosa Δ4AQ strain grown in LB with HQNO

label_protocol: cDNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix). Affymetrix WT terminal labeling kit was used with 1.5ug cDNA for fragmentation and labeling

growth_protocol: P. aeruginosa Δ4AQ were inoculated at an OD600 of 0.01 into 20 ml of LB medium in the absence or in the presence of 40 μM AQs or 1 mM IPTG. The cultures where grown at 37°C with  shaking (200 rpm) until they reached an OD600 of approximately 1.5

extract_protocol: Total RNA was isolated using the minelute RNA extraction kit (Qiagen), according to the manufacturer protocol, followed by DNaseI treatment (Roche).

treatment_protocol: Cells were harvested by centrifugation (1 ml of cultures) and RNA protect bacteria (Qiagen) was added according to the manufacturer protocol.

tag: protocol

value: LB with HQNO


title: Δ4AQ strain grown in LB with HQNO, biological rep 2

description: cells grown to OD600 of 1.5


title: 121s_D14


title: Mouse Rbp4+ PFC/OFC cells 1000700901_G2__IL699-710-518_S224


title: 196s_N3


title: Δ4AQ strain grown in LB with IPTG, biological rep 2

description: cells grown to OD600 of 1.5

source_name: P. aeruginosa Δ4AQ strain grown in LB with IPTG

value: LB with IPTG


title: Δ4AQ strain grown in LB with IPTG, biological rep 1

description: cells grown to OD600 of 1.5


title: Δ4AQ strain grown in LB with PQS, biological rep 1

description: cells grown to OD600 of 1.5

source_name: P. aeruginosa Δ4AQ strain grown in LB with PQS

value: LB with PQS


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C5_S235


title: Mouse Rbp4+ PFC/OFC cells 1000700901_G1__IL699-707-518_S223


title: Mouse Rbp4+ PFC/OFC cells 1000700901_G10__IL699-718-518_S230


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C4_S234


title: Δ4AQ strain grown in LB, biological rep 1

description: cells grown to OD600 of 1.5

source_name: P. aeruginosa Δ4AQ strain grown in LB

value: LB


title: 813s_K13


title: Δ4AQ strain grown in LB, biological rep 2

description: cells grown to OD600 of 1.5


title: Δ4AQ strain grown in LB with HHQ, biological rep 1

description: cells grown to OD600 of 1.5

source_name: P. aeruginosa Δ4AQ strain grown in LB with HHQ

value: LB with HHQ


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C3_S233


title: Mouse Rbp4+ PFC/OFC cells 1000700901_G11__IL699-719-518_S231


title: Mouse Rbp4+ PFC/OFC cells 1000700901_F9__IL699-705-518_S221


title: MOPS 5days T Replicate 1

city: Bern

first: Norbert

last: Polacek

address: Freiestrasse 3

department: Chemistry and Biochemistry

country: Switzerland

institute: University of Bern

description:
Bacterial cells were grown in MOPS media for 5 days. Cells were harvested by centrifugation and total RNA was extracted by hot acid phenole extraction. RNA was then size extracted by polyacrylamide gel electrophoresis (20-300nt range).
HLRPI2
small RNA 20-300nt

data_processing:
Triming of extra nucleotides and adapters by Cutadapt (cut-off phred quality score=30)
Alignment to reference genome by Bowtie2
Sam_sort: Alignments with too many mismatches and reads with too many genomic alignments are discarded.
Pseudo_se: paired ends alignments are merged into pseudo SE alignments
Identification of processing products was done by Flaimapper version 3 and featurecounts
Clustering: bam file is parsed using pybam (converted to Pyhton3).
Representative processing products are quantified and reported by parsing SAM files for every library
Genome_build: E.coli MG1655

organism: Escherichia coli str. K-12 substr. MG1655

source_name: RNA

growth_protocol: E.coli MG1655 carrying a pETgfp-mut2-AGGAGG plasmid were grown in LB and MOPS media supplemented with Kanamycin (25 µg/ml) and samples were harvested at OD600=0.4 (for cells grown in LB and MOPs), 48 hrs (for cells grown in LB), and 5 days (for cells grown in MOPS).

extract_protocol:
Samples from all conditions were used for total RNA extraction as well as for crude ribosome extraction. RNA was further extracted from crude ribosome pellets. Next, RNA was size selected after denaturing polyacrylamide gel electrophoresis (20-300nt).
Library constructuction was done with theTruSeq Small RNA Library Prep kit as per manufacturer's guidelines.

treatment_protocol: 2 biological replicates were collected for each condition.

tag: growth medium

value: MOPS

tag: rna source

value: Total RNA

tag: growth phase

value: Samples were extracted 5 days after first inoculation representing cells growing in stationary phase.


title: 298s_A10


title: Mouse Rbp4+ PFC/OFC cells 1000700901_F8__IL699-704-518_S220


title: MOPS 5days T Replicate 2

description:
Bacterial cells were grown in MOPS media for 5 days. Cells were harvested by centrifugation and total RNA was extracted by hot acid phenole extraction. RNA was then size extracted by polyacrylamide gel electrophoresis (20-300nt range).
HL4RPI17
small RNA 20-300nt


title: 682s_D6


title: 121s_G16


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C6_S236


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C23_S253


title: Mouse Rbp4+ PFC/OFC cells 1000700901_F7__IL699-703-518_S219


title: MOPS 5days R Replicate 2

description:
Bacterial cells were grown in MOPS media for 5 days. Cells were harvested by centrifugation and pellets were opened using a FastPrep. Lysates were cleared by centrifugation and loaded on a density gradient for Ultracentrifugation. Fractions containg polysomes were pooled and RNA was extracted via acid phenol extraction.
HL4RPI34
small RNA 20-300nt

value: Crude ribosome


title: Δ4AQ strain grown in LB with PQS, biological rep 2

description: cells grown to OD600 of 1.5


title: MOPS 5days R Replicate 1

description:
Bacterial cells were grown in MOPS media for 5 days. Cells were harvested by centrifugation and pellets were opened using a FastPrep. Lysates were cleared by centrifugation and loaded on a density gradient for Ultracentrifugation. Fractions containg polysomes were pooled and RNA was extracted via acid phenol extraction.
HLRPI16
small RNA 20-300nt


title: Mouse Rbp4+ PFC/OFC cells 1000700901_F6__IL699-702-518_S218


title: MOPS 0.4 T Replicate 2

description:
Bacterial cells were grown in MOPS media to OD = 0.4. Cells were harvested by centrifugation and total RNA was extracted by hot acid phenole extraction. RNA was then size extracted by polyacrylamide gel electrophoresis (20-300nt range).
HL4RPI9
small RNA 20-300nt

value: Samples were extracted at OD600=0.4 representing cells growing in exponential phase


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C22_S252


title: Mouse Rbp4+ PFC/OFC cells 1000700901_F5__IL699-701-518_S217


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C20_S250


title: MOPS 0.4 R Replicate 1

description:
Bacterial cells were grown in MOPS media to OD = 0.4. Cells were harvested by centrifugation and pellets were opened using a FastPrep. Lysates were cleared by centrifugation and loaded on a density gradient for Ultracentrifugation. Fractions containg polysomes were pooled and RNA was extracted via acid phenol extraction.
HLRPI18
small RNA 20-300nt


title: Mouse Rbp4+ PFC/OFC cells 1000700901_F4__IL699-729-507_S216


title: Mouse Rbp4+ PFC/OFC cells 1000700901_F2__IL699-728-507_S215


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C2_S232


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C1_S231


title: MOPS 0.4 R Replicate 2

description:
Bacterial cells were grown in MOPS media to OD = 0.4. Cells were harvested by centrifugation and pellets were opened using a FastPrep. Lysates were cleared by centrifugation and loaded on a density gradient for Ultracentrifugation. Fractions containg polysomes were pooled and RNA was extracted via acid phenol extraction.
HL4RPI10
small RNA 20-300nt


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C19_S249


title: Mouse Rbp4+ PFC/OFC cells 1000700901_F1__IL699-727-507_S214


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C18_S248


title: Mouse Rbp4+ PFC/OFC cells 1000700901_F12__IL699-706-518_S222


title: LB 48 hrs T Replicate 2

description:
Bacterial cells were grown in LB media to OD = 0.4. Cells were harvested by centrifugation and total RNA was extracted by hot acid phenole extraction. RNA was then size extracted by polyacrylamide gel electrophoresis (20-300nt range).
HL4RPI3
small RNA 20-300nt

value: Samples were extracted 48 hours after first inoculation representing cells growing in stationary phase.


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C21_S251


title: Mouse Rbp4+ PFC/OFC cells 1000700901_E9__IL699-723-507_S211


title: MOPS 0.4 T Replicate 1

description:
Bacterial cells were grown in MOPS media to OD = 0.4. Cells were harvested by centrifugation and total RNA was extracted by hot acid phenole extraction. RNA was then size extracted by polyacrylamide gel electrophoresis (20-300nt range).
HLRPI17
small RNA 20-300nt


title: LB 48hrs R Replicate 1

description:
Bacterial cells were grown in LB media for 48hrs. Cells were harvested by centrifugation and pellets were opened using a FastPrep. Lysates were cleared by centrifugation and loaded on a density gradient for Ultracentrifugation. Fractions containg polysomes were pooled and RNA was extracted via acid phenol extraction.
HLRPI12
small RNA 20-300nt


title: G2R3_Cortex_WT

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

country: United Kingdom

institute: UK Dementia Research Institute at Cardiff University

data_processing:
FastQC tool was used to evaluate the quality of the data.
Trimmomatic software was employed to filter poor quality reads and remove Illumina adapters.
Transcriptome annotation was carried out using tophat2, samtools and R software (GenomicFeatures, GenomicAlignments, Rsamtools)
Filtering: Genes that displayed zero variance across samples and those that had a cumulative RPKM value of less than five across all samples were discarded, leaving total of 16894 protein coding genes.
Data was normalized using TMM using calcNormFactors function from EdgeR library
Genome_build: mm10
Supplementary_files_format_and_content: "Raw_gene_counts_cortex.txt" contains the Tab delimited raw counts matrix

molecule: polyA RNA

source_name: Insular cortex

growth_protocol: Mice were housed in a 22°C–24 °C environment with a 12/12 light or dark cycle with water and food ad libitum, except when stated otherwise.

extract_protocol:
Insular cortex was bilaterally dissected and tissue from both hemispheres were agregated into a single sample per animal. All samples were stored in RNA-Later at -80°C until further analysis. RNA samples were prepared using standard poly-A isolation protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Prior to tissue sample collection, animals were tested for learning and memory performance at 2, 7, 8, 11 and 14 months of age using conditioned taste aversion (CTA) assay (PMID: 27103531)

value: WT

value: Insular cortex

tag: age

value: 7 m


title: G2R2_Cortex_WT


title: LB 48hrs R Replicate 2

description:
Bacterial cells were grown in LB media for 48hrs. Cells were harvested by centrifugation and pellets were opened using a FastPrep. Lysates were cleared by centrifugation and loaded on a density gradient for Ultracentrifugation. Fractions containg polysomes were pooled and RNA was extracted via acid phenol extraction.
HL4RPI5
small RNA 20-300nt


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C17_S247


title: Δ4AQ strain grown in LB with HHQ, biological rep 2

description: cells grown to OD600 of 1.5


title: Mouse Rbp4+ PFC/OFC cells 1000700901_E8__IL699-722-507_S210


title: LB 0.4 T Replicate 2

description:
Bacterial cells were grown in LB media for 48hrs. Cells were harvested by centrifugation and total RNA was extracted by hot acid phenole extraction. RNA was then size extracted by polyacrylamide gel electrophoresis (20-300nt range).
HL4RPI1
small RNA 20-300nt


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C15_S245


title: G2R7_Cortex_3xTgAD


title: Mouse Rbp4+ PFC/OFC cells 1000700901_E7__IL699-721-507_S209


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C14_S244


title: LB 0.4 T Replicate 1

description:
Bacterial cells were grown in LB media for 48hrs. Cells were harvested by centrifugation and total RNA was extracted by hot acid phenole extraction. RNA was then size extracted by polyacrylamide gel electrophoresis (20-300nt range).
HLRPI10
small RNA 20-300nt


title: LB 48hrs T Replicate 1

description:
Bacterial cells were grown in LB media to OD = 0.4. Cells were harvested by centrifugation and total RNA was extracted by hot acid phenole extraction. RNA was then size extracted by polyacrylamide gel electrophoresis (20-300nt range).
HLRPI13
small RNA 20-300nt


title: Ad-TFEB treated-rep3

city: Ann Arbor

first: Haocheng

last: Lu

state: Michigan

address: 2800 plymouth road

department: Internal Medicine

institute: University of Michigan

hyb_protocol: Following labeling procedure, 5.2 ug of cDNA were hybridized at 48C on Human Gene 2.1 ST.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: Data was analyzed using the oligo and limma Bioconductor package implemented in the R-statistical language version 3.4.0. RMA was used to fit log2 transformed expression values.

organism: Homo sapiens

source_name: HASMC

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: HASMCs (Lonza, CC-2571) were cultured in Smooth Muscle Cell Growth Medium 2 (Promo Cell C-22062)

extract_protocol: Total RNA was extracted with RNeasy mini kit according to the manufacturer's instructions (Qiagen).

treatment_protocol: HASMCs were infected with control adenovirus LacZ (Ad-LacZ) or adenovirus overexpressing TFEB (Ad-TFEB)  at multiplicities of infection of 30. Forty eight hours later, cells were collected for RNA extraction.

tag: cell type

value: human aortic smooth muscle cells

tag: passage

tag: adenovirus

value: overexpressing TFEB (Ad-TFEB)


title: LB 0.4 R Replicate 2

description:
Bacterial cells were grown in LB media to OD = 0.4. Cells were harvested by centrifugation and pellets were opened using a FastPrep. Lysates were cleared by centrifugation and loaded on a density gradient for Ultracentrifugation. Fractions containg polysomes were pooled and RNA was extracted via acid phenol extraction.
HL4RPI2
small RNA 20-300nt


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C13_S243


title: Ad-TFEB treated-rep1


title: LB 0.4 R Replicate 1

description:
Bacterial cells were grown in LB media to OD = 0.4. Cells were harvested by centrifugation and pellets were opened using a FastPrep. Lysates were cleared by centrifugation and loaded on a density gradient for Ultracentrifugation. Fractions containg polysomes were pooled and RNA was extracted via acid phenol extraction.
HLRPI11
small RNA 20-300nt


title: G2R6_Cortex_3xTgAD


title: G2R5_Cortex_3xTgAD


title: Ad-TFEB treated-rep2


title: Ad-LacZ treated-rep1

value: control LacZ (Ad-LacZ)


title: Mouse Rbp4+ PFC/OFC cells 1000700901_E4__IL699-718-507_S206


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C16_S246


title: Mouse Rbp4+ PFC/OFC cells 1000700901_E5__IL699-719-507_S207


title: RNAiD - 3fold [93432]

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

description: 18-30 nt size selection for miRNA seq

data_processing:
Basecalling RTA 1.18.64.0
The adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG) was cut once with cutadapt (v1.2.1).
The random 4mers on 5' and 3' were removed with fastx_trimmer of the fastx-toolkit (v0.0.13). The processed reads were filtered in respect of their size selection (18-30nt).
All reads were aligned to the C.elegans genome with tailor (v1.1). The minimum length of exact match was 18.
The random nucleotides (functioning as UMIs) within reads mapped to miRNAs and spike-ins were counted with htseq-count (v0.6.1p1).
Genome_build: WBcel235
Supplementary_files_format_and_content: count data as tab separated text

organism: Caenorhabditis elegans

source_name: embryos - 3-fold stage

extract_protocol:
Total RNA was extracted from embryo, L1 larvae, or arabidposis flowers collected in Trizol using a phenol-chloroform-based standard protocol. Small RNA sequencing libraries were constructed from an input of 25-75 embryos, corresponding to an estimated amount of 10-20 ng total RNA
RNA libraries were constructed as described in Alberti et al., 2018, Nature Methods. Given the low RNA input the protocol was modified: Less 5'- and 3' linker were used (500 nM final reaction concentration)

tag: treatment

value: RNAiD treatment (20 degree)

value: pash-1:AID, drsh-1:AID, sun-1p:TIR1, eft-3p:TIR1 + mirtrons

tag: developmental stage

value: Embryo (3-fold)


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C11_S241


title: Ad-LacZ treated-rep3


title: Mouse Rbp4+ PFC/OFC cells 1000700901_E3__IL699-716-507_S205


title: Ad-LacZ treated-rep2


title: G2R4_Cortex_WT


title: G5R5_Cortex_WT


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C12_S242


title: G3R10_Cortex_WT

value: 8 m


title: RNAiD - 3fold [88509]

description: 18-30 nt size selection for miRNA seq


title: Mouse Rbp4+ PFC/OFC cells LLJL10_C10_S240


title: G5R6_Cortex_WT


title: G5R4_Cortex_WT


title: pash-1(ts) - 3fold - #2 [86508]

description: 18-30 nt size selection for miRNA seq

value: pash-1(ts) restrictive (25 degree)

value: pash-1(ts) [mj100] + mirtrons


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B8_S215


title: Mouse Rbp4+ PFC/OFC cells 1000700901_E6__IL699-720-507_S208


title: pash-1(ts) - 3fold - #1 [93440]

description: 18-30 nt size selection for miRNA seq


title: Mouse Rbp4+ PFC/OFC cells 1000700901_E12__IL699-726-507_S213


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B6_S213


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B7_S214


title: G5R3_Cortex_3xTgAD


title: Mouse Rbp4+ PFC/OFC cells 1000700901_E11__IL699-724-507_S212


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B5_S212


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B4_S211


title: G5R1_Cortex_3xTgAD


title: G4R7_Cortex_WT


title: Mouse Rbp4+ PFC/OFC cells 1000700901_D8__IL699-711-507_S201


title: N2 - 3fold - #1 [86498]

description: 18-30 nt size selection for miRNA seq

source_name: embryos - 3-fold

value: control sample - (20 degree)

value: wild type


title: RNAiD - L1 - #1 [88510]

description: 88510_GAGTGG_CDMBFANXX_1_20190510B_20190510

source_name: whole L1 larvae

extract_protocol:
Total RNA was extracted from embryo, L1 larvae, or arabidposis flowers collected in Trizol using a phenol-chloroform-based standard protocol. Small RNA sequencing libraries were constructed from an input of 25-75 embryos, corresponding to an estimated amount of 10-20 ng total RNA
RNA libraries were constructed as described in Alberti et al., 2018, Nature Methods. Given the low RNA input the protocol was modified: Less 5'- and 3' linker were used (500 nM final reaction concentration)
18-30 nt size selection for miRNA seq

value: pash-1:AID, drsh-1:AID, sun-1p:TIR1, eft-3p:TIR1

tag: developmental stage/tissue

value: Larval 1 (L1)


title: Mouse Rbp4+ PFC/OFC cells 1000700901_D7__IL699-710-507_S200


title: RNAiD - Gastrulation - #2 [86502]

description: 86502_TAGCTT_CDNATANXX_3_20190416B_20190416

source_name: embryos - Gastrulation

value: Embryo (Gastrulation)


title: RNAiD - Gastrulation - #1 [86501]

description: 86501_GATCAG_CDNATANXX_3_20190416B_20190416


title: Mouse Rbp4+ PFC/OFC cells 1000700901_D6__IL699-707-507_S199


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B2_S209


title: Mouse Rbp4+ PFC/OFC cells 1000700901_E1__IL699-714-507_S203


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B3_S210


title: Mouse Rbp4+ PFC/OFC cells 1000700901_D5__IL699-706-507_S198


title: G4R6_Cortex_WT

value: WT


title: Mouse Rbp4+ PFC/OFC cells 1000700901_E2__IL699-715-507_S204


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B23_S230


title: G4R5_Cortex_WT

value: Insular cortex


title: G4R3_Cortex_3xTgAD


title: RNAiD - 2cell - #2 [86500]

description: 86500_ACTTGA_CDNATANXX_3_20190416B_20190416

source_name: embryos - 2-cell stage

value: Embryo (2-cell stage)


title: RNAiD - 2cell - #1 [86499]

description: 86499_CAGATC_CDNATANXX_3_20190416B_20190416


title: G4R2_Cortex_3xTgAD


title: RNAiD - L1 - #2 [86503]

description: 86503_GGCTAC_CDNATANXX_3_20190416B_20190416


title: Mouse Rbp4+ PFC/OFC cells 1000700901_D12__IL699-712-507_S202


title: G5R2_Cortex_3xTgAD


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B22_S229


title: pash-1(ts) - L1 - #2 [88508]

description: 88508_GTTTCG_CDMBFANXX_1_20190510B_20190510


title: G4R1_Cortex_3xTgAD


title: pash-1(ts) - L1 - #1 [88507]

description: 88507_GTGGCC_CDMBFANXX_1_20190510B_20190510


title: pash-1(ts) - Gastrulation - #1 [86506]

description: 86506_AGTTCC_CDNATANXX_3_20190416B_20190416


title: G1R5_Cortex_WT

value: 2 m


title: pash-1(ts) - 2cell - #2 [88506]

description: 88506_GTGAAA_CDMBFANXX_1_20190510B_20190510


title: G1R7_Cortex_WT


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B21_S228


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B20_S227


title: Mouse Rbp4+ PFC/OFC cells 1000700901_D3__IL699-704-507_S196


title: Mouse Rbp4+ PFC/OFC cells 1000700901_D4__IL699-705-507_S197


title: Mouse Rbp4+ PFC/OFC cells 1000700901_C4__IL699-724-517_S188


title: pash-1(ts) - Gastrulation - #2 [86507]

description: 86507_ATGTCA_CDNATANXX_3_20190416B_20190416


title: G1R6_Cortex_WT


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B19_S226


title: Mouse Rbp4+ PFC/OFC cells 1000700901_C5__IL699-726-517_S189


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B1_S208


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B18_S225


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B16_S223


title: pash-1(ts) - 2cell - #1 [88505]

description: 88505_GTAGAG_CDMBFANXX_1_20190510B_20190510


title: G1R2_Cortex_3xTgAD


title: Mouse Rbp4+ PFC/OFC cells 1000700901_C1__IL699-723-517_S187


title: Mouse Rbp4+ PFC/OFC cells 1000700901_D2__IL699-703-507_S195


title: G3R9_Cortex_WT


title: N2 - L1 - #2 [88504]

description: 88504_CCGTCC_CDMBFANXX_1_20190510B_20190510


title: N2 - L1 - #1 [88503]

description: 88503_ATGTCA_CDMBFANXX_1_20190510B_20190510


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B17_S224


title: Mouse Rbp4+ PFC/OFC cells 1000700901_C12__IL699-702-507_S194


title: Mouse Rbp4+ PFC/OFC cells 1000700901_C11__IL699-701-507_S193


title: Mouse Rbp4+ PFC/OFC cells 1000700901_C8__IL699-728-517_S191


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B15_S222


title: N2 - Gastrulation - #2 [86497]

description: 86497_ACAGTG_CDNATANXX_3_20190416B_20190416


title: G1R4_Cortex_3xTgAD


title: G3R7_Cortex_WT


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B14_S221


title: N2 - Gastrulation - #1 [86505]

description: 86505_AGTCAA_CDNATANXX_3_20190416B_20190416


title: Mouse Rbp4+ PFC/OFC cells 1000700901_C10__IL699-729-517_S192


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B13_S220


title: Mouse Rbp4+ PFC/OFC cells 1000700901_B8__IL699-719-517_S183


title: G1R3_Cortex_3xTgAD


title: G3R3_Cortex_3xTgAD


title: G3R4_Cortex_3xTgAD


title: Mouse Rbp4+ PFC/OFC cells 1000700901_B5__IL699-716-517_S181


title: N2 - 2cell - #1 [86510]

description: 86510_GTGAAA_CDNATANXX_3_20190416B_20190416


title: Mouse Rbp4+ PFC/OFC cells 1000700901_B6__IL699-718-517_S182


title: N2 - 2cell - #2 [86496]

description: 86496_TGACCA_CDNATANXX_3_20190416B_20190416


title: G3R1_Cortex_3xTgAD


title: Mouse Rbp4+ PFC/OFC cells 1000700901_B4__IL699-715-517_S180


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B11_S218


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B10_S217


title: Oct4-ChIP-seq

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

library_source: genomic

data_processing:
ChIP-nexus data processing steps: Random barcodes and fixed barcodes were trimmed off the reads and reassigned to FASTQ labels using nimnexus (v0.1.1). The adapters were then trimmed using cutadapt (v1.8.1).
Reads were aligned with BWA (v0.7.13) using the command bwa aln -q 5 -l 32 -k to the mouse genome assembly mm10. Mapping stats were computed using SAMtools flagstat (v1.2). Mutant samples were aligned to a modified mm10 genome that accommodated the CRISPR changes.
Reads were filtered using SAMtools view to remove unmapped reads and mates, non-primary alignments, reads failing platform or vendor quality checks, and PCR or optical duplicates (-F 1804). Low quality reads (MAPQ < 30) were also removed. Reads aligned to the same position with the same barcode, CIGAR string and the SAM flag were de-duplicated using nimnexus dedup (v0.1.1).
The final filtered BAM file was converted to tagAlign format (BED 3+3) using bedtools `bamtobed` (v2.26) (126). Cross-correlation scores were obtained for each file using phantompeakqualtools (v1.2).
BigWig tracks containing the strand-specific number of aligned 5' read ends (pooled across all replicates) were generated using bedtools genomecov -5 -bg -strand <+/->, followed by bedGraph to BigWig conversion using UCSC bedGraphToBigWig.
Peaks were called using MACS2 (v2.1.1.20160309) by shifting and extending the reads to obtain coverage tracks similar to ChIP-seq (shift=-75, extsize=150). Peaks overlaping the blacklisted regions listed in  http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz were excluded. Peak calling was performed on different combinations of aligned reads from different replicate experiments as described in Landt et al. 2012 and as used in the ENCODE ChIP-seq pipeline. Finally, 1kb regions centered at peak summits from the "optimal set" of reproducible, ranked consistent peaks passing the Irreproducible Discovery Rate (IDR) threshold of 0.05 were used as the peak regions for the corresponding TF (i.e. peaks that are reproducible and rank consistently across replicates).
ChIP-seq datasets were processed using the ENCODE ChIP-seq pipeline https://github.com/ENCODE-DCC/chip-seq-pipeline2/releases/tag/v1.2.2. The ChIP-seq pipeline is identical to the ChIP-nexus pipeline described above except that it uses the SPP peak caller and doesn't use barcodes for read de-duplication.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig tracks containing the strand-specific number of aligned 5' read ends (pos=+ strand, neg=- strand) were generated using bedtools genomecov -5 -bg -strand <+/->, followed by bedGraph to BigWig conversion using UCSC bedGraphToBigWig.
Supplementary_files_format_and_content: Bed files contain the "optimal'' peaks passing the IDR threshold of 0.05 as described above.

molecule: genomic DNA

growth_protocol: Mouse R1 ESCs were cultured on 0.1% gelatin-coated plates without feeder cells. Mouse ESC medium was prepared by supplementing N2B27 medium (1:1 mix of DMEM/F12 with GlutaMax supplemented with N2 and Neurobasal medium supplemented with B27, Invitrogen) with 2 mM L-Glutamine (Stemcell Technologies), 1x 2‑Mercaptoethanol (Millipore), 1x NEAA (Stemcell Technologies), 3 µM CHIR99021 (Stemcell Technologies), 1 µM PD0325901 (Stemcell Technologies), 0.033% BSA solution (Invitrogen) and 107 U/ml LIF (Millipore).

extract_protocol:
For each ChIP experiment, 107 mouse ESCs were used. Cells were washed with PBS and cross-linked with 1% formaldehyde (Fisher Scientific) in PBS for 10 min at room temperature. The reaction was quenched with 125 mM glycine. Fixed cells were washed with cold PBS, scraped, centrifuged, resuspended in cold lysis buffer (15 mM HEPES (pH 7.5), 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.5% N‑lauroylsarcosine, 0.1% sodium deoxycholate, 0.1% SDS), incubated for 10 min on ice and sonicated with a Bioruptor Pico for four cycles of 30 s on and 30 s off.  ChIP-seq experiments were performed as previously described in Koenecke et al 2017 "Drosophila poised enhancers are generated during tissue patterning with the help of repression" with 107  mouse ESCs per ChIP. For each ChIP, 5 µg of the following antibodies were used: ɑ-Oct3/4 (Santa Cruz, sc-8628), ɑ-Sox2 (Santa Cruz, sc-17320), or ɑ-Nanog (Santa Cruz, sc-30328). At least two biological replicates were performed for each factor. Single-end sequencing was performed on either an Illumina HiSeq instrument (50 cycles) or NextSeq 500 instrument (75 cycles) according to manufacturer’s instructions.
Sequencing libraries were prepared for sequencing using standard Illumina protocols
The ChIP-nexus procedure and data processing were performed as previously described in Johnston et al 2015 except that the ChIP-nexus adaptor mix contained four fixed barcodes (ACTG, CTGA, GACT, TGAC). For each ChIP, 5 µg antibody was coupled to 50 µl of Dynabeads Protein A or Protein G (Invitrogen). The following antibodies were used: ɑ-Oct3/4 (Santa Cruz, sc-8628), ɑ-Sox2 (Santa Cruz, sc-17320), ɑ-Nanog (Santa Cruz, sc-30328), ɑ-Klf4 (R&D Systems, AF3158), ɑ-Klf4 (Abcam, ab106629), ɑ-Esrrb (Abcam, ab19331), ɑ-Pbx 1/2/3 (Santa Cruz, sc-888), and ɑ-Zic3 (Abcam, ab222124).

tag: cell line

value: R1 ESCs

value: embryonic stem cells

tag: chip antibody

value: anti-Oct3/4 (Santa Cruz, sc-8628)


title: Mouse Rbp4+ PFC/OFC cells 1000700901_B12__IL699-722-517_S186

tag: genotype


title: HASMC_AdBAF60a_2

data_processing:
FastQC (Babraham Bioinformatics) was used for quality control of the sequencing reads from each sample.
The human reference cDNA sequences were downloaded from the Ensembl database (GRCh38 ftp://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/cdna/).
The reference was indexed with Salmon v 0.14.0, and gene expression quantification was performed using Salmon in its nonalignment-based mode.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include count and TPM value for each sample

source_name: Human aortic smooth muscle cells

growth_protocol: Primary human aortic smooth muscle cells (HASMCs, CC-2571) were purchased from Lonza (Walkersville, MD). HASMCs were cultured in Smooth Muscle Cell Growth Medium 2 (PromoCell, Germany) containing 5% fetal bovine serum at 37°C in humidified incubator 5% CO2.

extract_protocol:
Total RNA from HASMCs was isolated with the RNeasy Mini Kit (QIAGEN, #74106) followed by treatment with RNase-free DNase I (QIAGEN, #79254).
RNA library preparation and sequencing were performed by the DNA sequencing core at the University of Michigan. Briefly, the RNA library was prepared with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced on a NovaSeq 6000 platform (Illumina) to generate pair-end 51 bp reads according to the manufacturer’s recommendation. In total, ~250 million reads were generated with an average of 31 million paired-reads per sample.

treatment_protocol: Primary HASMCs were infected with 20MOI AdBAF60a (adenovirus encoding human BAF60a) or AdGFP

value: Primary vascular smooth muscle cells

tag: passages

tag: race

value: Caucasion

value: 22 years old

tag: Sex

value: male


title: HASMC_siBAF60a_3

source_name: Human Aortic smooth muscle cells

extract_protocol:
Total RNA from HASMCs was isolated with the RNeasy Mini Kit (QIAGEN, #74106) followed by treatment with RNase-free DNase I (QIAGEN, #79254).
RNA library preparation and sequencing were performed by the DNA sequencing core at the University of Michigan. Briefly, the RNA library was prepared with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced on a HiSeq 4000 platform (Illumina) to generate single-end 51 bp reads according to the manufacturer’s recommendation. In total, ~350 million reads were generated with an average of 43 million single-reads per sample.

treatment_protocol: Primary HASMCs were transfected with 30nM siBAF60a (ThermoFisher Scientific, # s13151) or non-targeting siRNA (Silencer™ Select Negative Control No. 1 siRNA, ThermoFisher Scientific, #4390843) using Lipofectamine RNAiMAX Reagent (Invitrogen, # 13778150)


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A7_S191

source_name: medial prefrontal cortex


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A9_S193


title: input-control-ChIP-seq

source_name: input-control-chipseq


title: HASMC_AdBAF60a_3


title: Mouse Rbp4+ PFC/OFC cells 1000700901_B3__IL699-714-517_S179


title: Mouse Rbp4+ PFC/OFC cells LLJL10_B12_S219


title: HASMC_AdGFP_2

value: AdGFP


title: Mouse Rbp4+ PFC/OFC cells 1000700901_B10__IL699-720-517_S184


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A4_S188


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A3_S187


title: HASMC_siControl_4

value: siControl


title: HASMC_siBAF60a_4


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A6_S190


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A5_S189


title: Mouse Rbp4+ PFC/OFC cells 1000700901_A9__IL699-705-517_S173


title: HASMC_AdBAF60a_1


title: Mouse Rbp4+ PFC/OFC cells 1000700901_B2__IL699-712-517_S178


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A8_S192


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A2_S186


title: Mouse Rbp4+ PFC/OFC cells 1000700901_B11__IL699-721-517_S185


title: HASMC_AdGFP_3


title: Mouse Rbp4+ PFC/OFC cells 1000700901_B1__IL699-711-517_S177


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A23_S207


title: HASMC_siBAF60a_2


title: HASMC_siBAF60a_1


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A22_S206


title: HASMC_AdGFP_1


title: Mouse Rbp4+ PFC/OFC cells 1000700901_A6__IL699-702-517_S170


title: Mouse Rbp4+ PFC/OFC cells 1000700901_A7__IL699-703-517_S171


title: HASMC_siBAF60a_DSG_BRG1

data_processing:
ChIP-seq reads were aligned to the human genome (NCBI GRCh19) using bowtie2 version 2.3.5 with default settings.
Peaks were called using MACS2 software and the reads from input served as a control with parameters: -f BAMPE -g hs -B --SPMR -q 0.05.
Samples were normalized to adjust for sequencing depth.
Genome_build: GRCh19
Supplementary_files_format_and_content: bigwig files were generated with UCCS tools 'bedGraphToBigWig' from the MACS2 .bdg file

extract_protocol:
Chromatin immunoprecipitation was performed with the SimpleChIP Enzymatic Chromatin IP Kit (#9003, CST), according to manufacturer’s recommendation. Histone-DNA complexes were isolated with antibodies against H3K9Ac (Cell Signaling, #9649, 1:100 dilution), H3K27Ac (Cell Signaling, #8173, 1:100 dilution) or BRG1 ( Abcam, ab110641, 1:100 dilution). The sample for BRG1 ChIPseq was crosslinked with 2mM disuccinimidyl glutarate (DSG, ThermoFisher Scientific, #20593) at room temperature for 45 min before paraformaldehyde crosslinking.
The DNA library preparation and sequencing were performed by the DNA sequencing core at the University of Michigan. Briefly, the DNA library was prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced on a NovaSeq 6000 S1 flowcell (Illumina) to generate pair-end 101 bp reads.

value: BRG1 (Abcam, ab110641)


title: HASMC_siBAF60a_DSG_input


title: Mouse Rbp4+ PFC/OFC cells 1000700901_A8__IL699-704-517_S172


title: HASMC_siControl_2


title: HASMC_siBAF60a_H3K9Ac

value: H3K9Ac (Cell Signaling, #9649)


title: HASMC_siControl_1


title: Mouse Rbp4+ PFC/OFC cells 1000700901_A4__IL699-729-506_S168


title: HASMC_siBAF60a_input


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A21_S205


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A19_S203


title: Mouse Rbp4+ PFC/OFC cells 1000700901_A5__IL699-701-517_S169


title: s_Sa2411_neg_2

city: New York

first: Sudha

last: Guttikonda

state: New York

address: 430 E 67th St

department: Developmental Biology

institute: MSKCC

data_processing:
library strategy: SMARTER-Seq
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s no -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file containing normalized counts

source_name: co-cultured hPSC-neurons

growth_protocol: Cells were co-cultured with neurons at either the progenitor stage or macrophage stage for 2 weeks with IL-34 and M-CSF.

extract_protocol:
CD45+CX3CR1+ cells were sorted from co-cultures, lysed in trizol, and extracted using the Zymo RNA Micro Prep kit.
Libraries were prepared according to Illumina's instructions.

tag: cell line/tissue source

value: Human WT iPSC cell line (SA2411)

value: hPSC-neuron

tag: protocol

value: hPSC-derived neurons sorted from co-cultures at day 40 of in vitro culture.

tag: replicate

value: Biological replicate SA2411 neurons 2


title: Mouse Rbp4+ PFC/OFC cells 1000700901_A12__IL699-710-517_S176


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A20_S204


title: s_Sa2411_neg_1

value: Biological replicate SA2411 neurons 1


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A1_S185


title: HASMC_siCtrl_DSG_input


title: HASMC_siControl_3


title: Mouse Rbp4+ PFC/OFC cells 1000700901_A1__IL699-728-506_S167


title: s_H9_neg_2

value: Human ES cell line (H9)

value: Biological replicate H9 neurons 2


title: s_H9_neg_1

value: Biological replicate H9 neurons 1


title: HASMC_siCtrl_DSG_BRG1


title: HASMC_siCtrl_H3K27Ac

value: H3K27Ac (Cell Signaling, #8173)


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A18_S202


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A17_S201


title: Mouse Rbp4+ PFC/OFC cells 1000700901_A11__IL699-707-517_S175


title: HASMC_siBAF60a_H3K27Ac

value: Primary vascular smooth muscle cells


title: s_H1_neg_3

value: Human ES cell line (H1)

value: Biological replicate H1 neurons 2


title: HASMC_siCtrl_H3K9Ac

value: Caucasion

value: 22 years old

value: male


title: Mouse Rbp4+ PFC/OFC cells 1000700901_A10__IL699-706-517_S174


title: HASMC_siCtrl_input


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A16_S200


title: E11_5_scRNA-Seq

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

institute: EMBL

data_processing:
Quality control of reads was done using the fastqc software.
reads were separated by cell barcodes making one file per cell.
Adapters were removed using cutadapt
alignment to the mouse genome mm10 (GRCm38.86) was done using STAR.
We counted reads that overlapped exactly with one gene.
We assumed that two UMI barcodes with a difference of two mismatches could originate from one. If there was such a pair where one of UMI barcodes had only 10% of reads from another one, we joined those reads considering it as one UMI. In this way, we reduced the amount of false-positive UMIs.
We created a UMI count matrix where columns were cells; rows were gene features. We did not include in a count matrix UMIs that had less than two reads. Later, we considered a gene to be expressed if it had at least one UMI.
Genome_build: mm10
Supplementary_files_format_and_content: E9_5_rawcounts_matrix.tsv: Matrix in TSV format containing the RNA raw counts on ensembl genes for YS and AGM at day 9.5.
Supplementary_files_format_and_content: E11_5_rawcounts_matrix.tsv: Matrix in TSV format containing the RNA raw counts on Ensembl genes for YS and AGM at day 11.5.
Supplementary_files_format_and_content: Metadata_E9_5.txt: File in TXT format containing three columns Cell-Barcode-State.
Supplementary_files_format_and_content: Metadata_E11_5.txt: File in TXT format containing three columns Cell-Barcode-State.

source_name: Embryo

extract_protocol:
Single cell suspensions of wild type AGM and YS at E9.5 and E11.5 were analyzed and sorted with flow cytometry.  After flow cytometry sorting, VE-CadPos and VE-CadNeg cells were stained with Hoechst 33342 (Cell Viability Imaging kit, Molecular Probes), and counted with the Moxi Z Mini Automated Cell Counter (ORFLO). Stained cell solution was diluted in a mix with diluent and RNase inhibitor (New England Biolabs) to 1 cell/50 nl for dispensing on the ICELL8-chip (Takara) with the MultiSample NanoDispenser (Takara). Positive (RNA from E14FF mouse embryonic stem cells) and negative controls were prepared according to the ICELL8 protocol and dispensed with the MSND into the respective nanowells of the chip. All nanowells of the ICELL8 chip were imaged with a fluorescence microscope (Olympus). The images were analysed with the CellSelect software (Takara). Live single cells positive for Hoechst-33342 were selected for lysis and reverse transcription inside the ICELL8 chip. RT reaction mix containing 5X RT buffer, dNTPs, RT e5- oligo (Takara), nuclease-free water, Maxima H Minus RT (Thermo Fisher Scientific) and Triton X100 was prepared and dispensed into the previously selected nanowells with single cells inside. The chip was placed inside a modified SmartChip Cycler (Bio-Rad) for the RT reaction (42°C for 90 min, 85°C for 5 min, 4°C forever). The cDNA of all single cells was collected together and further concentrated with the DNA Clean and Concentrator−5 kit (Zymo Research). The Exonuclease I (New England Biolabs) reaction of the cDNA (37°C for 30 min, 80°C for 20 min, 4°C forever) was performed inside a conventional thermal cycler. Afterwards, the cDNA was amplified with the Advantage 2 PCR Kit (Clontech Takara) containing buffer, dNTPs, Amp Primer (Takara), polymerase mix and nucleasefree water (95°C for 1 min, 18 cycles of 95°C for 15 s, 65°C for 30 s and 68°C for 6 min, followed by 72°C for 10 min and 4°C forever). The amplified cDNA was purified with Ampure XP Beads (Beckmann Coulter). The cDNA size distribution was obtained with the High Sensitivity DNA BioAnalyzer (Agilent) and quantification was performed with the Qubit (Life Technologies).
Illumina library preparation was carried out by using Nextera XT DNA (Illumina). Tagmentation was performed in tagment DNA buffer, Amplicon Tagment Mix and 1 ng of purified cDNA (55°C for 5 min and 10°C forever), next Neutralize Tagment Buffer was added (room temperature for 5 min.). After incubation, the NexteraXT PCR reaction mix was prepared with Nextera PCR Mastermix, i7 Index Primer from the Nextera Index Kit (Illumina), Nextera Primer P5 and Tagmented cDNA-NT buffer mix (72°C for 3 min, 95°C for 30 s, 12 cycles of 95°C for 10 s, 55°C for 30 s and 72°C for 30 s, final 72°C for 5 min and 10°C forever). Ampure XP purification was performed with the finished library. The size distribution was checked on an Agilent BioAnalyzer. Samples were sequenced with the Illumina NextSeq 500 sequencer using the SMARTer ICELL8 Single-Cell System protocol (paired-end 3’ end sequencing with UMIs).

tag: development stage

tag: tissue

value: Yolk Sac and Aorta-Gonad-Mesonephros

value: wildtype


title: s_H1_neg_2

tag: cell type

value: Biological replicate H1 neurons 1


title: E9_5_scRNA-Seq


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A15_S199


title: Day4_macro_co-culture

data_processing:
SEQC pipeline was used for: count matrix generation from Illumina fastq files (intermediate steps: cell barcode and UMI extraction, merging of forward and reverse fastq, alignment with STAR, barcode correction,  resolving of multi-aligning reads, alignment error correction, count matrix generation, filtering out of 1) empty droplets based on library size distribution; 2) dying cells based on abundance of mitochodrial RNA; 3) low complexity cells based on ratio of number of genes detected  over library size, see methods of paper)
only for pre-processed files: count matrix normalization and log transformation as described in paper (normalization of counts to 10,000 RNA molecules per cell, followed by log transformation of counts using natural log and pseudo-count 1)
only for pre-processed files: second cell filtering round as described in paper (removal of putative empty droplets, dying cells and cells differentiating into types not of interest)
Genome_build: hg38
Supplementary_files_format_and_content: csv containing normalized counts

source_name: hPSC-microglia from co-culture with hPSC-neurons

growth_protocol: Cells were cultured in hematopoietic cytokines (VEGF, FGF2, SCF, IL6, IL3, TPO) during the in vitro differentiation.

extract_protocol:
Dissociated cells were strained through a 40uM filter and resuspended at 1000 cells/uL in FACS buffer.
Libraries were prepared according to the 10x genomics Chromium Single Cell 3' Library & Gel bead Kit V2 according to manufacturer's protocol.

tag: cell line source

value: hPSC-microglia

value: Day 10 progenitors were matured to primitive macrophages in IL-34 and M-CSF and then co-cultured with neurons for 4 days.

tag: dissociation

value: accutase


title: s_42_human_primary

source_name: Postmortem brain tissue

value: Postmortem brain tissue

value: Primary human microglia

value: Biological replicate primary 3


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A14_S198


title: Day8_suspension

source_name: Day 10 of in vitro microglial differentiation

value: primitive hematopoietic cells

value: Later primitive hematopoietic cells (Day 10) were cultured in the presence of SCF, IL6, TPO, and IL3 for 4 days.

value: Trituration of cells in suspension


title: s_39_human_primary

value: Biological replicate primary 2


title: Nanog-ChIP-seq

source_name: Nanog-chipseq

value: R1 ESCs

value: embryonic stem cells

value: anti-Nanog (Santa Cruz, sc-30328)


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A12_S196


title: Day8_accutase

value: Human ES cell line (H1)

value: primitive hematopoietic cells and hemogenic endothelium


title: s_23_human_primary

value: Biological replicate primary 1


title: Zic3-ChIP-nexus

value: anti-Zic3 (Abcam, ab222124)


title: Day4

source_name: Day 6 of in vitro microglial differentiation

value: Early primitive hematopoietic cells and hemogenic endothelium

value: Early primitive hematopoietic precursors (Day 6) were cultured in the presence of VEGF, FGF2, SCF, and IL-6 for 4 days.


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A13_S197


title: s_Sa2411_macro_2

source_name: Macro co-culture derived hPSC-microglia

value: Human WT iPSC cell line (SA2411)

value: hPSC-microglia

value: Day 10 progenitors were matured to primitive macrophages in IL-34 and M-CSF and then co-cultured with neurons for 2 weeks.

value: Biological replicate SA2411 macro 2


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A11_S195


title: s_Sa2411_macro_1

value: Biological replicate Sa2411 macro 1


title: s_43_human_primary

value: Postmortem brain tissue

value: Primary human microglia

value: Biological replicate primary 4


title: HASMCs HPbCD_3

data_processing:
The quality control of the sequencing reads from each sample was assessed with FastQC (Babraham Bioinformatics).
The human reference cDNA sequences were downloaded from the Ensembl database (GRCh38 ftp://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/cdna/).
The reference was indexed with Salmon v 0.14.0, and gene expression quantification was performed using Salmon in its nonalignment-based mode.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include count and TPM value for each sample

growth_protocol: Human aortic smooth muscle cells (HASMCs, CC-2571) were purchased from Lonza (Walkersville, MD). HASMCs were cultured in Smooth Muscle Cell Growth Medium 2 (Promo Cell, Germany) at 37°C/5% CO2 humidified incubator.

extract_protocol:
Total RNA was extracted from cells using RNeasy Mini Kit (74106, QIAGEN, Hilden, Germany)
RNA library preparation and sequencing were performed by the DNA sequencing core at the University of Michigan. Briefly, the RNA library was prepared with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced on a NovaSeq 6000 platform (Illumina) to generate pair-end 51 bp reads according to the manufacturer’s recommendation. In total, ~250 million reads were generated with an average of 31 million paired-reads per sample.

treatment_protocol: At 80% confluence, cells were treated with either control (PBS) or HPbCD (10mg/mL) for 24 hours.

value: primay vascular smooth muscle cells

tag: passage

tag: treatment

value: HPbCD 10 mg/mL


title: Pbx-ChIP-nexus

source_name: Pbx

value: R1 ESCs

value: embryonic stem cells

value: anti-Pbx 1/2/3 (Santa Cruz, sc-888)


title: s_H9_macro_2

value: Human ES cell line (H9)

value: Biological replicate H9 macro 1


title: patchcap

data_processing:
Random barcodes and fixed barcodes were trimmed off the reads and reassigned to FASTQ labels using nimnexus (v0.1.1). The adapters were then trimmed using cutadapt (v1.8.1).
Reads were aligned with BWA (v0.7.13) using the command bwa aln -q 5 -l 32 -k to the mouse genome assembly mm10. Mapping stats were computed using SAMtools flagstat (v1.2). Mutant samples were aligned to a modified mm10 genome that accommodated the CRISPR changes.
Reads were filtered using SAMtools view to remove unmapped reads and mates, non-primary alignments, reads failing platform or vendor quality checks, and PCR or optical duplicates (-F 1804). Low quality reads (MAPQ < 30) were also removed. Reads aligned to the same position with the same barcode, CIGAR string and the SAM flag were de-duplicated using nimnexus dedup (v0.1.1).
The final filtered BAM file was converted to tagAlign format (BED 3+3) using bedtools `bamtobed` (v2.26) (126). Cross-correlation scores were obtained for each file using phantompeakqualtools (v1.2).
BigWig tracks containing the strand-specific number of aligned 5' read ends (pooled across all replicates) were generated using bedtools genomecov -5 -bg -strand <+/->, followed by bedGraph to BigWig conversion using UCSC bedGraphToBigWig.
Peaks were called using MACS2 (v2.1.1.20160309) by shifting and extending the reads to obtain coverage tracks similar to ChIP-seq (shift=-75, extsize=150). Peaks overlaping the blacklisted regions listed in  http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz were excluded. Peak calling was performed on different combinations of aligned reads from different replicate experiments as described in Landt et al. 2012 and as used in the ENCODE ChIP-seq pipeline. Finally, 1kb regions centered at peak summits from the "optimal set" of reproducible, ranked consistent peaks passing the Irreproducible Discovery Rate (IDR) threshold of 0.05 were used as the peak regions for the corresponding TF (i.e. peaks that are reproducible and rank consistently across replicates).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig tracks containing the strand-specific number of aligned 5' read ends (pos=+ strand, neg=- strand) were generated using bedtools genomecov -5 -bg -strand <+/->, followed by bedGraph to BigWig conversion using UCSC bedGraphToBigWig.
Supplementary_files_format_and_content: Bed files contain the "optimal'' peaks passing the IDR threshold of 0.05 as described above.

source_name: embryonic stem cells

extract_protocol:
For each ChIP experiment, 107 mouse ESCs were used. Cells were washed with PBS and cross-linked with 1% formaldehyde (Fisher Scientific) in PBS for 10 min at room temperature. The reaction was quenched with 125 mM glycine. Fixed cells were washed with cold PBS, scraped, centrifuged, resuspended in cold lysis buffer (15 mM HEPES (pH 7.5), 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.5% N‑lauroylsarcosine, 0.1% sodium deoxycholate, 0.1% SDS), incubated for 10 min on ice and sonicated with a Bioruptor Pico for four cycles of 30 s on and 30 s off.
Sequencing libraries were prepared for sequencing using standard Illumina protocols
The ChIP-nexus procedure and data processing were performed as previously described in Johnston et al 2015 except that the ChIP-nexus adaptor mix contained four fixed barcodes (ACTG, CTGA, GACT, TGAC). For each ChIP, 5 µg antibody was coupled to 50 µl of Dynabeads Protein A or Protein G (Invitrogen). The following antibodies were used: ɑ-Oct3/4 (Santa Cruz, sc-8628), ɑ-Sox2 (Santa Cruz, sc-17320), ɑ-Nanog (Santa Cruz, sc-30328), ɑ-Klf4 (R&D Systems, AF3158), ɑ-Klf4 (Abcam, ab106629), ɑ-Esrrb (Abcam, ab19331), ɑ-Pbx 1/2/3 (Santa Cruz, sc-888), and ɑ-Zic3 (Abcam, ab222124).


title: Mouse Rbp4+ PFC/OFC cells LLJL10_A10_S194

extract_protocol:
mPFC or OFC was dissected form acute slices of the mouse brain. Samples were digested and cells released by tirturation. TdTomato+ cells were FACS sorted into 384 well plates
smartseq2


title: Essrb-ChIP-nexus

source_name: Esrrb

value: anti-Esrrb (Abcam, ab19331)


title: HASMCs HPbCD_2


title: Klf4-ChIP-nexus

value: anti-Klf4 (R&D Systems, AF3158)


title: s_H1_macro_2

value: Human ES cell line (H1)

value: Biological replicate H1 macro 2


title: HASMCs HPbCD_1


title: s_H1_macro_3

value: hPSC-microglia

value: Day 10 progenitors were matured to primitive macrophages in IL-34 and M-CSF and then co-cultured with neurons for 2 weeks.

value: Biological replicate H1 macro 3


title: HASMCs Control_4

value: PBS


title: s_H1_macro_1

value: Biological replicate H1 macro 1