title: E18.5_ctrl5_cell158


title: E18.5_ctrl5_cell150

status: Public on Aug 25 2023

type: SRA

city: Stockholm

first: Kasra

last: Nikouei

address: Solnav. 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description:
SmartSeq2
Munguba_Nikouei_E18.5_counts.txt
Munguba_Nikouei_E18.5_cell_annotation.txt

library_source: transcriptomic single cell

data_processing:
Fastq files demultiplexed by deindexer (https://github.com/ws6/deindexer) using the Nextera index adapters and the 384-well layout. Individual fastq files were then mapped to the genome assembly using the STAR aligner (Dobin et al. 2013; DOI:10.1093/bioinformatics/bts635) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads. The expression values were computed per gene as described in (Ramsköld et al. 2009; DOI: 10.1371/journal.pcbi.1000598 ), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. 2013; DOI: 10.1371/journal.pone.0053822). The count matrix shows the individual counts aligning to each gene per cell.
genome build: mm10
Tab-delimited text format, in which cells make up the columns and genes the rows, with corresponding cell annotation file.

molecule: polyA RNA

organism: Mus musculus

source_name: Neocortex

extract_protocol:
Embryonic day 18.5 (E18.5) pups were extracted after sacrificing SstCre/+::R26R CAG-boosted eGFP (RCE)/+::Sox6fl/± females with plugged pregnancies. The neocortices of the pups were dissected in ice-cold HBSS. Genotyping of the pups were done in parallel by using QuickExtract DNA Solution (Lucigen). The tissue was dissociated into a single cell suspension, as previously described (Muñoz-Manchado et al. 2018; DOI: 10.1016/j.celrep.2018.07.053). Briefly, the tissue was dissociated using the Papain dissociation system (Worthington) following the manufacturer’s instructions. Cell suspension obtained was filtered with 20 μm filter and kept in cold oxygenated Hank's balanced salt solution (HBSS) with 0.2% Bovine Serum Albumin (BSA). EGFP positive but DRAQ7 negative (dead cell marker, Invitrogen) cells were FACS sorted into 384-well plates containing lysis buffer and processed in large accordance with the Smartseq2 protocol (Picelli et al. 2014; DOI: 10.1038/nprot.2014.006).
The libraries were generated according to the Smartseq2 protocol (Picelli et al., 2014; DOI: 10.1038/nprot.2014.006). The single-cell transcriptome data was generated at the Eukaryotic Single-cell Genomics facility at Science for Life Laboratory in Stockholm, Sweden.

tag: tissue

value: Neocortex

tag: age

tag: cell type

value: Somatostatin interneuron

tag: genotype

value: SstCre::RCE::Sox6 +/+


title: E18.5_ctrl5_cell144


title: E18.5_ctrl5_cell145


title: E18.5_ctrl5_cell139


title: E18.5_ctrl5_cell140


title: E18.5_ctrl5_cell138


title: E18.5_ctrl5_cell137


title: E18.5_ctrl5_cell135


title: E18.5_ctrl5_cell142


title: E18.5_ctrl5_cell152


title: E18.5_ctrl5_cell136


title: E18.5_ctrl5_cell153


title: E18.5_ctrl5_cell133


title: E18.5_ctrl5_cell134


title: E18.5_ctrl5_cell141


title: E18.5_ctrl5_cell126


title: E18.5_ctrl5_cell131


title: E18.5_ctrl5_cell127


title: E18.5_ctrl5_cell130


title: E18.5_ctrl5_cell124


title: E18.5_ctrl5_cell132


title: E18.5_ctrl5_cell125


title: E18.5_ctrl5_cell128


title: E18.5_ctrl5_cell120


title: E18.5_ctrl5_cell121


title: E18.5_ctrl5_cell119


title: E18.5_ctrl5_cell123


title: E18.5_ctrl5_cell113


title: E18.5_ctrl5_cell117


title: E18.5_ctrl5_cell118


title: E18.5_ctrl5_cell116


title: E18.5_ctrl5_cell114


title: E18.5_ctrl5_cell111


title: E18.5_ctrl5_cell115


title: E18.5_ctrl5_cell109


title: E18.5_ctrl5_cell105


title: E18.5_ctrl5_cell112


title: E18.5_ctrl5_cell106


title: E18.5_ctrl5_cell108


title: E18.5_ctrl5_cell107


title: E18.5_ctrl5_cell129


title: E18.5_ctrl5_cell104


title: E18.5_ctrl5_cell99


title: E18.5_ctrl5_cell98


title: E18.5_ctrl5_cell100


title: E18.5_ctrl5_cell101


title: E18.5_ctrl5_cell102


title: E18.5_ctrl5_cell97


title: E18.5_ctrl5_cell110


title: E18.5_ctrl5_cell94


title: E18.5_ctrl5_cell91


title: E18.5_ctrl5_cell89


title: E18.5_ctrl5_cell90


title: E18.5_ctrl5_cell92


title: E18.5_ctrl5_cell88


title: E18.5_ctrl5_cell87


title: E18.5_ctrl5_cell85


title: E18.5_ctrl5_cell84


title: E18.5_ctrl5_cell83


title: E18.5_ctrl5_cell80


title: E18.5_ctrl5_cell82


title: E18.5_ctrl5_cell81


title: E18.5_ctrl5_cell79


title: E18.5_ctrl5_cell78


title: E18.5_ctrl5_cell86


title: E18.5_ctrl5_cell103


title: E18.5_ctrl5_cell95


title: E18.5_ctrl5_cell77


title: E18.5_ctrl5_cell96


title: E18.5_ctrl5_cell74


title: E18.5_ctrl5_cell75


title: E18.5_ctrl5_cell76


title: E18.5_ctrl5_cell70


title: E18.5_ctrl5_cell71


title: E18.5_ctrl5_cell69


title: E18.5_ctrl5_cell73


title: E18.5_ctrl5_cell68


title: E18.5_ctrl5_cell122


title: E18.5_ctrl5_cell63


title: E18.5_ctrl5_cell64


title: E18.5_ctrl5_cell61


title: E18.5_ctrl5_cell62


title: E18.5_ctrl5_cell60


title: E18.5_ctrl5_cell66


title: E18.5_ctrl5_cell59


title: E18.5_ctrl5_cell93


title: E18.5_ctrl5_cell57


title: E18.5_ctrl5_cell54


title: E18.5_ctrl5_cell56


title: E18.5_ctrl5_cell55


title: E18.5_ctrl5_cell53


title: E18.5_ctrl5_cell72


title: E18.5_ctrl5_cell58


title: E18.5_ctrl5_cell50


title: E18.5_ctrl5_cell51


title: E18.5_ctrl5_cell48


title: E18.5_ctrl5_cell52


title: E18.5_ctrl5_cell44


title: E18.5_ctrl5_cell49


title: E18.5_ctrl5_cell47


title: E18.5_ctrl5_cell45


title: E18.5_ctrl5_cell42


title: E18.5_ctrl5_cell46


title: E18.5_ctrl5_cell41


title: E18.5_ctrl5_cell40


title: E18.5_ctrl5_cell36


title: E18.5_ctrl5_cell35


title: E18.5_ctrl5_cell38


title: E18.5_ctrl5_cell34


title: E18.5_ctrl5_cell33


title: E18.5_ctrl5_cell32


title: E18.5_ctrl5_cell37


title: E18.5_ctrl5_cell28


title: E18.5_ctrl5_cell31


title: E18.5_ctrl5_cell30


title: E18.5_ctrl5_cell27


title: E18.5_ctrl5_cell26


title: E18.5_ctrl5_cell25


title: E18.5_ctrl5_cell24


title: E18.5_ctrl5_cell23


title: E18.5_ctrl5_cell43


title: E18.5_ctrl5_cell18


title: E18.5_ctrl5_cell39


title: E18.5_ctrl5_cell22


title: E18.5_ctrl5_cell17


title: E18.5_ctrl5_cell16


title: E18.5_ctrl5_cell15


title: E18.5_ctrl5_cell14


title: E18.5_ctrl5_cell13


title: E18.5_ctrl5_cell9


title: E18.5_ctrl5_cell11


title: E18.5_ctrl5_cell8


title: E18.5_ctrl5_cell10


title: E18.5_ctrl5_cell12


title: E18.5_ctrl5_cell7


title: E18.5_ctrl5_cell6


title: E18.5_ctrl5_cell5


title: E18.5_ctrl5_cell3


title: E18.5_ctrl5_cell4


title: E18.5_ctrl5_cell2


title: E18.5_ctrl5_cell29


title: E18.5_ctrl5_cell19


title: E18.5_ctrl5_cell21


title: E18.5_ctrl5_cell1


title: E18.5_ctrl5_cell20


title: E18.5_ctrl5_cell67


title: E18.5_ctrl4_cell187

value: SstCre::RCE::Sox6 +/-


title: E18.5_ctrl4_cell183


title: E18.5_ctrl4_cell190


title: E18.5_ctrl4_cell186


title: E18.5_ctrl4_cell188


title: E18.5_ctrl4_cell185


title: E18.5_ctrl4_cell181


title: E18.5_ctrl4_cell180


title: E18.5_ctrl4_cell179


title: E18.5_ctrl4_cell178


title: E18.5_ctrl4_cell175


title: E18.5_ctrl4_cell174


title: E18.5_ctrl4_cell177


title: E18.5_ctrl4_cell176


title: E18.5_ctrl4_cell172


title: E18.5_ctrl4_cell173


title: E18.5_ctrl4_cell171


title: E18.5_ctrl4_cell167


title: E18.5_ctrl4_cell170


title: E18.5_ctrl4_cell189


title: E18.5_ctrl4_cell169


title: E18.5_ctrl4_cell166


title: E18.5_ctrl4_cell182


title: E18.5_ctrl4_cell165


title: E18.5_ctrl4_cell184


title: E18.5_ctrl4_cell163


title: E18.5_ctrl4_cell164


title: E18.5_ctrl4_cell158


title: E18.5_ctrl4_cell161


title: E18.5_ctrl4_cell162


title: E18.5_ctrl4_cell160


title: E18.5_ctrl4_cell159


title: E18.5_ctrl4_cell155


title: E18.5_ctrl4_cell168


title: E18.5_ctrl4_cell157


title: E18.5_ctrl4_cell154


title: E18.5_ctrl4_cell153


title: E18.5_ctrl4_cell149


title: E18.5_ctrl4_cell151


title: E18.5_ctrl4_cell150


title: E18.5_ctrl4_cell148


title: E18.5_ctrl4_cell147


title: E18.5_ctrl4_cell146


title: E18.5_ctrl4_cell145


title: E18.5_ctrl4_cell143


title: E18.5_ctrl4_cell144


title: E18.5_ctrl4_cell141


title: E18.5_ctrl4_cell156


title: E18.5_ctrl4_cell138


title: E18.5_ctrl4_cell140


title: E18.5_ctrl4_cell135


title: E18.5_ctrl4_cell136


title: E18.5_ctrl4_cell132


title: E18.5_ctrl4_cell139


title: E18.5_ctrl4_cell152


title: E18.5_ctrl4_cell130


title: E18.5_ctrl4_cell129


title: E18.5_ctrl4_cell131


title: E18.5_ctrl4_cell134


title: E18.5_ctrl4_cell128


title: E18.5_ctrl4_cell121


title: C3

status: Public on Aug 26 2023

city: Leuven

first: Lies

last: Van Horebeek

address: Herestraat 49

department: Neurosciences

country: Belgium

institute: KU Leuven

description:
First sample of B lymphocytes of MS patient, targeted scRNAseq, 10 µl input cDNA, 20 PCR cycles
CCL5, CD38, ICOSLG, S100A11, TREX1 mRNA
Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics)

data_processing:
Downsampled datasets were obtained through random downsampling of fastq filesl with seqtk-1.3.
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1.
Tagging sequences were extracted from the BAM files outputted by Cell Ranger using samtools and awk commands, and merged while tracking associated transcript and dataset.
Genotypes were called in individual transcripts using VarTrix v1.1.3 in debugging mode.
Assembly: hg19
Supplementary files format and content: Tab separated text files, tsv files and matrix counts

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
PBMCs were isolated from peripheral blood in EDTA containing tubes using lymphoprep. B cells or CD8+ T cells were enriched using EasySep Human B Cell or CD8+ T cell Isolation Kits (STEMCELL Technologies).
Libraries were constructed according to the manufacturer's instructions (10x Genomics, Chromium Next GEM Single Cell 3' Reagents Kit) or with our in-house developed targeted sequencing method.

value: peripheral blood

value: B lymphocytes


title: E18.5_ctrl4_cell120


title: E18.5_ctrl4_cell127


title: E18.5_ctrl4_cell118


title: E18.5_ctrl4_cell125


title: E18.5_ctrl4_cell133


title: E18.5_ctrl4_cell112


title: E18.5_ctrl4_cell124


title: E18.5_ctrl4_cell122


title: E18.5_ctrl4_cell123


title: E18.5_ctrl4_cell111


title: E18.5_ctrl4_cell105


title: E18.5_ctrl4_cell119


title: E18.5_ctrl4_cell108


title: E18.5_ctrl4_cell142


title: E18.5_ctrl4_cell126


title: E18.5_ctrl4_cell137


title: E18.5_ctrl4_cell116


title: E18.5_ctrl4_cell103


title: E18.5_ctrl4_cell115


title: E18.5_ctrl4_cell114


title: E18.5_ctrl4_cell109


title: E18.5_ctrl4_cell110


title: E18.5_ctrl4_cell100


title: E18.5_ctrl4_cell98


title: E18.5_ctrl4_cell106


title: E18.5_ctrl4_cell104


title: E18.5_ctrl4_cell99


title: E18.5_ctrl4_cell102


title: E18.5_ctrl4_cell90


title: E18.5_ctrl4_cell95


title: E18.5_ctrl4_cell91


title: E18.5_ctrl4_cell89


title: E18.5_ctrl5_cell65


title: E18.5_ctrl4_cell88


title: E18.5_ctrl4_cell107


title: E18.5_ctrl4_cell96


title: E18.5_ctrl4_cell87


title: E18.5_ctrl4_cell85


title: E18.5_ctrl4_cell83


title: E18.5_ctrl4_cell117


title: E18.5_ctrl4_cell82


title: E18.5_ctrl4_cell81


title: E18.5_ctrl4_cell86


title: E18.5_ctrl4_cell84


title: E18.5_ctrl4_cell80


title: E18.5_ctrl4_cell97


title: E18.5_ctrl4_cell79


title: E18.5_ctrl4_cell78


title: E18.5_ctrl4_cell113


title: E18.5_ctrl4_cell92


title: E18.5_ctrl4_cell75


title: E18.5_ctrl4_cell73


title: E18.5_ctrl4_cell77


title: E18.5_ctrl4_cell74


title: E18.5_ctrl4_cell93


title: E18.5_ctrl4_cell76


title: E18.5_ctrl4_cell94


title: E18.5_ctrl4_cell71


title: E18.5_ctrl4_cell70


title: E18.5_ctrl4_cell72


title: E18.5_ctrl4_cell67


title: E18.5_ctrl4_cell69


title: E18.5_ctrl4_cell66


title: E18.5_ctrl4_cell65


title: E18.5_ctrl4_cell68


title: E18.5_ctrl4_cell64


title: E18.5_ctrl4_cell62


title: E18.5_ctrl4_cell58


title: E18.5_ctrl4_cell101


title: E18.5_ctrl4_cell63


title: E18.5_ctrl4_cell61


title: E18.5_ctrl4_cell59


title: E18.5_ctrl4_cell57


title: E18.5_ctrl4_cell55


title: E18.5_ctrl4_cell56


title: E18.5_ctrl4_cell60


title: E18.5_ctrl4_cell53


title: E18.5_ctrl4_cell54


title: E18.5_ctrl4_cell43


title: E18.5_ctrl4_cell50


title: E18.5_ctrl4_cell48


title: E18.5_ctrl4_cell44


title: E18.5_ctrl4_cell42


title: E18.5_ctrl4_cell35


title: E18.5_ctrl4_cell41


title: E18.5_ctrl4_cell40


title: E18.5_ctrl4_cell34


title: E18.5_ctrl4_cell39


title: E18.5_ctrl4_cell36


title: E18.5_ctrl4_cell37


title: E18.5_ctrl4_cell47


title: E18.5_ctrl4_cell45


title: E18.5_ctrl4_cell52


title: E18.5_ctrl4_cell49


title: E18.5_ctrl4_cell46


title: E18.5_ctrl4_cell38


title: E18.5_ctrl4_cell32


title: E18.5_ctrl4_cell29


title: E18.5_ctrl4_cell31


title: E18.5_ctrl4_cell30


title: E18.5_ctrl4_cell26


title: E18.5_ctrl4_cell24


title: E18.5_ctrl4_cell27


title: E18.5_ctrl4_cell28


title: E18.5_ctrl4_cell25


title: E18.5_ctrl4_cell51


title: E18.5_ctrl4_cell21


title: E18.5_ctrl4_cell22


title: E18.5_ctrl4_cell33


title: E18.5_ctrl4_cell19


title: E18.5_ctrl4_cell20


title: E18.5_ctrl4_cell16


title: E18.5_ctrl4_cell11


title: E18.5_ctrl4_cell8


title: E18.5_ctrl4_cell12


title: E18.5_ctrl4_cell17


title: E18.5_ctrl4_cell5


title: E18.5_ctrl4_cell18


title: E18.5_ctrl4_cell7


title: E18.5_ctrl4_cell15


title: E18.5_ctrl4_cell14


title: E18.5_ctrl4_cell23


title: E18.5_ctrl4_cell13


title: E18.5_ctrl4_cell6


title: E18.5_ctrl4_cell10


title: E18.5_ctrl4_cell9


title: E18.5_ctrl4_cell4


title: E18.5_ctrl4_cell3


title: E18.5_mut4_cell383

value: SstCre::RCE::Sox6 flox/-


title: E18.5_mut4_cell384


title: E18.5_ctrl4_cell2


title: E18.5_mut4_cell381


title: E18.5_mut4_cell382


title: E18.5_mut4_cell379


title: E18.5_mut4_cell374


title: E18.5_mut4_cell380


title: E18.5_mut4_cell375


title: E18.5_mut4_cell377


title: E18.5_mut4_cell376


title: E18.5_mut4_cell365


title: E18.5_mut4_cell370


title: E18.5_mut4_cell360


title: E18.5_mut4_cell372


title: E18.5_mut4_cell358


title: E18.5_mut4_cell361


title: E18.5_mut4_cell369


title: E18.5_mut4_cell373


title: E18.5_mut4_cell368


title: E18.5_mut4_cell367


title: E18.5_mut4_cell378


title: E18.5_mut4_cell362


title: E18.5_ctrl4_cell1


title: E18.5_mut4_cell359


title: E18.5_mut4_cell352


title: E18.5_mut4_cell371


title: E18.5_mut4_cell363


title: E18.5_mut4_cell357


title: E18.5_mut4_cell349


title: E18.5_mut4_cell354


title: E18.5_mut4_cell353


title: E18.5_mut4_cell350


title: E18.5_mut4_cell351


title: E18.5_mut4_cell348


title: E18.5_mut4_cell339


title: E18.5_mut4_cell341


title: E18.5_mut4_cell347


title: E18.5_mut4_cell338


title: E18.5_mut4_cell356


title: E18.5_mut4_cell346


title: E18.5_mut4_cell366


title: E18.5_mut4_cell337


title: E18.5_mut4_cell336


title: E18.5_mut4_cell345


title: E18.5_mut4_cell364


title: E18.5_mut4_cell342


title: E18.5_mut4_cell344


title: E18.5_mut4_cell329


title: E18.5_mut4_cell328


title: E18.5_mut4_cell327


title: E18.5_mut4_cell340


title: E18.5_mut4_cell325


title: E18.5_mut4_cell355


title: E18.5_mut4_cell323


title: E18.5_mut4_cell335


title: E18.5_mut4_cell333


title: E18.5_mut4_cell331


title: E18.5_mut4_cell334


title: E18.5_mut4_cell321


title: E18.5_mut4_cell330


title: E18.5_mut4_cell326


title: E18.5_mut4_cell324


title: E18.5_mut4_cell343


title: E18.5_mut4_cell316


title: E18.5_mut4_cell315


title: E18.5_mut4_cell311


title: E18.5_mut4_cell310


title: E18.5_mut4_cell322


title: E18.5_mut4_cell332


title: E18.5_mut4_cell314


title: E18.5_mut4_cell320


title: E18.5_mut4_cell317


title: E18.5_mut4_cell307


title: E18.5_mut4_cell303


title: E18.5_mut4_cell301


title: E18.5_mut4_cell306


title: E18.5_mut4_cell312


title: E18.5_mut4_cell308


title: E18.5_mut4_cell313


title: E18.5_mut4_cell299


title: E18.5_mut4_cell305


title: E18.5_mut4_cell300


title: E18.5_mut4_cell304


title: E18.5_mut4_cell298


title: E18.5_mut4_cell302


title: E18.5_mut4_cell319


title: E18.5_mut4_cell296


title: E18.5_mut4_cell318


title: E18.5_mut4_cell291


title: E18.5_mut4_cell297


title: E18.5_mut4_cell295


title: E18.5_mut4_cell290


title: E18.5_mut4_cell289


title: E18.5_mut4_cell293


title: E18.5_mut4_cell292


title: E18.5_mut4_cell286


title: E18.5_mut4_cell294


title: E18.5_mut4_cell309


title: E18.5_mut4_cell287


title: E18.5_mut4_cell284


title: E18.5_mut4_cell285


title: E18.5_mut4_cell288


title: E18.5_mut4_cell282


title: E18.5_mut4_cell283


title: E18.5_mut4_cell278


title: E18.5_mut4_cell280


title: E18.5_mut4_cell275


title: E18.5_mut4_cell276


title: E18.5_mut4_cell281


title: E18.5_mut4_cell279


title: E18.5_mut4_cell271


title: E18.5_mut4_cell268


title: E18.5_mut4_cell274


title: E18.5_mut4_cell269


title: E18.5_mut4_cell267


title: E18.5_mut4_cell270


title: E18.5_mut4_cell263


title: E18.5_mut4_cell264


title: E18.5_mut4_cell266


title: E18.5_mut4_cell262


title: E18.5_mut4_cell258


title: E18.5_mut4_cell265


title: E18.5_mut4_cell260


title: E18.5_mut4_cell273


title: E18.5_mut4_cell277


title: E18.5_mut4_cell261


title: E18.5_mut4_cell255


title: E18.5_mut4_cell251


title: E18.5_mut4_cell257


title: E18.5_mut4_cell250


title: E18.5_mut4_cell256


title: E18.5_mut4_cell259


title: E18.5_mut4_cell254


title: E18.5_mut4_cell272


title: E18.5_mut4_cell253


title: E18.5_mut4_cell242


title: E18.5_mut4_cell249


title: E18.5_mut4_cell247


title: E18.5_mut4_cell239


title: E18.5_mut4_cell237


title: E18.5_mut4_cell238


title: E18.5_mut4_cell245


title: E18.5_mut4_cell241


title: E18.5_mut4_cell234


title: E18.5_mut4_cell244


title: E18.5_mut4_cell232


title: E18.5_mut4_cell248


title: E18.5_mut4_cell243


title: E18.5_mut4_cell240


title: E18.5_mut4_cell252


title: E18.5_mut4_cell246


title: E18.5_mut4_cell236


title: E18.5_mut4_cell235


title: E18.5_mut4_cell230


title: E18.5_mut4_cell231


title: E18.5_mut4_cell227


title: E18.5_mut4_cell233


title: E18.5_mut4_cell229


title: E18.5_mut4_cell225


title: E18.5_mut4_cell222


title: E18.5_mut4_cell218


title: E18.5_mut4_cell215


title: E18.5_mut4_cell214


title: E18.5_mut4_cell228


title: E18.5_mut4_cell224


title: E18.5_mut4_cell223


title: E18.5_mut4_cell211


title: E18.5_mut4_cell221


title: E18.5_mut4_cell208


title: E18.5_mut4_cell206


title: E18.5_mut4_cell220


title: E18.5_mut4_cell219


title: E18.5_mut4_cell213


title: E18.5_mut4_cell204


title: E18.5_mut4_cell212


title: E18.5_mut4_cell209


title: E18.5_mut4_cell210


title: E18.5_mut4_cell202


title: E18.5_mut4_cell226


title: E18.5_mut4_cell207


title: E18.5_mut4_cell198


title: E18.5_mut4_cell200


title: E18.5_mut4_cell201


title: E18.5_mut4_cell203


title: E18.5_mut4_cell199


title: E18.5_mut4_cell192


title: E18.5_mut4_cell194


title: E18.5_mut4_cell191


title: E18.5_mut4_cell188


title: E18.5_mut4_cell197


title: E18.5_mut4_cell217


title: E18.5_mut4_cell196


title: E18.5_mut4_cell216


title: E18.5_mut4_cell195


title: E18.5_mut4_cell186


title: E18.5_mut4_cell190


title: E18.5_mut4_cell189


title: E18.5_mut4_cell187


title: E18.5_mut4_cell193


title: E18.5_mut4_cell205


title: E18.5_mut4_cell183


title: E18.5_mut4_cell184


title: E18.5_mut4_cell180


title: E18.5_mut4_cell182


title: E18.5_mut4_cell179


title: E18.5_mut4_cell178


title: E18.5_mut4_cell185


title: E18.5_mut4_cell173


title: E18.5_mut4_cell172


title: E18.5_mut4_cell174


title: E18.5_mut4_cell177


title: E18.5_mut4_cell176


title: E18.5_mut4_cell165


title: E18.5_mut4_cell163


title: E18.5_mut4_cell181


title: E18.5_mut4_cell170


title: E18.5_mut4_cell169


title: E18.5_mut4_cell168


title: E18.5_mut4_cell167


title: E18.5_mut4_cell158


title: E18.5_mut4_cell160


title: E18.5_mut4_cell156


title: E18.5_mut4_cell166


title: E18.5_mut4_cell152


title: E18.5_mut4_cell171


title: E18.5_mut4_cell162


title: E18.5_mut4_cell149


title: E18.5_mut4_cell150


title: E18.5_mut4_cell164


title: E18.5_mut4_cell146


title: E18.5_mut4_cell161


title: E18.5_mut4_cell157


title: E18.5_mut4_cell175


title: E18.5_mut4_cell144


title: E18.5_mut4_cell155


title: E18.5_mut4_cell145


title: E18.5_mut4_cell159


title: E18.5_mut4_cell154


title: E18.5_mut4_cell148


title: E18.5_mut4_cell147


title: E18.5_mut4_cell151


title: E18.5_mut4_cell140


title: E18.5_mut4_cell141


title: E18.5_mut4_cell139


title: E18.5_mut4_cell138


title: E18.5_mut4_cell136


title: E18.5_mut4_cell143


title: E18.5_mut4_cell134


title: E18.5_mut4_cell142


title: E18.5_mut4_cell153


title: E18.5_mut4_cell137


title: E18.5_mut4_cell130


title: E18.5_mut4_cell133


title: E18.5_mut4_cell132


title: E18.5_mut4_cell131


title: E18.5_mut4_cell129


title: E18.5_mut4_cell128


title: E18.5_mut4_cell126


title: E18.5_mut4_cell122


title: E18.5_mut4_cell127


title: E18.5_mut4_cell125


title: E18.5_mut4_cell123


title: E18.5_mut4_cell120


title: E18.5_mut4_cell121


title: E18.5_mut4_cell119


title: E18.5_mut4_cell135


title: E18.5_mut4_cell114


title: E18.5_mut4_cell115


title: E18.5_mut4_cell112


title: E18.5_mut4_cell117


title: E18.5_mut4_cell108


title: E18.5_mut4_cell116


title: E18.5_mut4_cell111


title: E18.5_mut4_cell105


title: E18.5_mut4_cell110


title: E18.5_mut4_cell113


title: E18.5_mut4_cell103


title: E18.5_mut4_cell102


title: E18.5_mut4_cell109


title: E18.5_mut4_cell106


title: E18.5_mut4_cell100


title: E18.5_mut4_cell124


title: E18.5_mut4_cell107


title: E18.5_mut4_cell98


title: E18.5_mut4_cell97


title: E18.5_mut4_cell95


title: E18.5_mut4_cell96


title: E18.5_mut4_cell101


title: E18.5_mut4_cell93


title: E18.5_mut4_cell91


title: E18.5_mut4_cell118


title: E18.5_mut4_cell104


title: E18.5_mut4_cell94


title: E18.5_mut4_cell92


title: E18.5_mut4_cell88


title: E18.5_mut4_cell90


title: E18.5_mut4_cell87


title: E18.5_mut4_cell86


title: E18.5_mut4_cell84


title: E18.5_mut4_cell85


title: E18.5_mut4_cell83


title: E18.5_mut4_cell82


title: E18.5_mut4_cell80


title: E18.5_mut4_cell77


title: E18.5_mut4_cell81


title: E18.5_mut4_cell79


title: E18.5_mut4_cell99


title: E18.5_mut4_cell78


title: E18.5_mut4_cell73


title: E18.5_mut4_cell76


title: E18.5_mut4_cell72


title: E18.5_mut4_cell70


title: E18.5_mut4_cell74


title: E18.5_mut4_cell69


title: E18.5_mut4_cell75


title: E18.5_mut4_cell67


title: E18.5_mut4_cell65


title: E18.5_mut4_cell89


title: E18.5_mut4_cell66


title: E18.5_mut4_cell71


title: E18.5_mut4_cell63


title: E18.5_mut4_cell64


title: E18.5_mut4_cell62


title: E18.5_mut4_cell60


title: E18.5_mut4_cell68


title: E18.5_mut4_cell61


title: E18.5_mut4_cell58


title: E18.5_mut4_cell57


title: E18.5_mut4_cell56


title: E18.5_mut4_cell55


title: E18.5_mut4_cell52


title: E18.5_mut4_cell54


title: E18.5_mut4_cell50


title: E18.5_mut4_cell53


title: E18.5_mut4_cell48


title: E18.5_mut4_cell49


title: E18.5_mut4_cell47


title: E18.5_mut4_cell45


title: E18.5_mut4_cell43


title: E18.5_mut4_cell46


title: E18.5_mut4_cell40


title: E18.5_mut4_cell38


title: E18.5_mut4_cell37


title: E18.5_mut4_cell39


title: E18.5_mut4_cell44


title: E18.5_mut4_cell36


title: E18.5_mut4_cell59


title: E18.5_mut4_cell42


title: E18.5_mut4_cell35


title: E18.5_mut4_cell51


title: E18.5_mut4_cell30


title: E18.5_mut4_cell31


title: E18.5_mut4_cell28


title: E18.5_mut4_cell32


title: E18.5_mut4_cell29


title: E18.5_mut4_cell27


title: E18.5_mut4_cell26


title: E18.5_mut4_cell25


title: E18.5_mut4_cell22


title: E18.5_mut4_cell20


title: E18.5_mut4_cell41


title: E18.5_mut4_cell19


title: E18.5_mut4_cell17


title: E18.5_mut4_cell16


title: E18.5_mut4_cell34


title: E18.5_mut4_cell15


title: E18.5_mut4_cell11


title: E18.5_mut4_cell14


title: E18.5_mut4_cell10


title: E18.5_mut4_cell12


title: E18.5_mut4_cell13


title: E18.5_mut4_cell33


title: E18.5_mut4_cell6


title: E18.5_mut4_cell9


title: E18.5_mut4_cell8


title: E18.5_mut4_cell7


title: E18.5_mut4_cell24


title: E18.5_mut4_cell5


title: E18.5_mut4_cell21


title: E18.5_mut4_cell3


title: E18.5_mut4_cell23


title: E18.5_mut4_cell4


title: E18.5_mut4_cell2


title: E18.5_mut4_cell18


title: E18.5_mut3_cell124

value: SstCre::RCE::Sox6 flox/flox


title: E18.5_mut3_cell125


title: E18.5_mut3_cell123


title: E18.5_mut3_cell126


title: E18.5_mut4_cell1


title: E18.5_mut3_cell122


title: E18.5_mut3_cell120


title: E18.5_mut3_cell121


title: E18.5_mut3_cell119


title: E18.5_mut3_cell118


title: E18.5_mut3_cell117


title: E18.5_mut3_cell116


title: E18.5_mut3_cell114


title: E18.5_mut3_cell115


title: E18.5_mut3_cell112


title: E18.5_mut3_cell110


title: E18.5_mut3_cell109


title: E18.5_mut3_cell108


title: E18.5_mut3_cell107


title: E18.5_mut3_cell106


title: E18.5_mut3_cell105


title: E18.5_mut3_cell104


title: E18.5_mut3_cell103


title: E18.5_mut3_cell101


title: E18.5_mut3_cell100


title: E18.5_mut3_cell96


title: E18.5_mut3_cell97


title: E18.5_mut3_cell98


title: E18.5_mut3_cell95


title: E18.5_mut3_cell93


title: E18.5_mut3_cell99


title: E18.5_mut3_cell91


title: E18.5_mut3_cell89


title: E18.5_mut3_cell94


title: E18.5_mut3_cell88


title: E18.5_mut3_cell92


title: E18.5_mut3_cell90


title: E18.5_mut3_cell111


title: E18.5_mut3_cell113


title: E18.5_mut3_cell87


title: E18.5_mut3_cell85


title: E18.5_mut3_cell86


title: E18.5_mut3_cell81


title: E18.5_mut3_cell83


title: E18.5_mut3_cell82


title: E18.5_mut3_cell84


title: E18.5_mut3_cell80


title: E18.5_mut3_cell79


title: E18.5_mut3_cell102


title: E18.5_mut3_cell78


title: E18.5_mut3_cell77


title: E18.5_mut3_cell75


title: E18.5_mut3_cell74


title: E18.5_mut3_cell73


title: E18.5_mut3_cell71


title: E18.5_mut3_cell70


title: E18.5_mut3_cell67


title: E18.5_mut3_cell65


title: E18.5_mut3_cell66


title: E18.5_mut3_cell69


title: E18.5_mut3_cell61


title: E18.5_mut3_cell62


title: E18.5_mut3_cell59


title: E18.5_mut3_cell64


title: E18.5_mut3_cell63


title: E18.5_mut3_cell57


title: E18.5_mut3_cell58


title: E18.5_mut3_cell55


title: E18.5_mut3_cell60


title: E18.5_mut3_cell56


title: E18.5_mut3_cell53


title: E18.5_mut3_cell54


title: E18.5_mut3_cell51


title: E18.5_mut3_cell76


title: E18.5_mut3_cell48


title: E18.5_mut3_cell49


title: E18.5_mut3_cell72


title: E18.5_mut3_cell47


title: E18.5_mut3_cell46


title: E18.5_mut3_cell45


title: E18.5_mut3_cell44


title: E18.5_mut3_cell43


title: E18.5_mut3_cell42


title: E18.5_mut3_cell41


title: E18.5_mut3_cell68


title: E18.5_mut3_cell38


title: E18.5_mut3_cell40


title: E18.5_mut3_cell37


title: E18.5_mut3_cell36


title: E18.5_mut3_cell39


title: E18.5_mut3_cell52


title: E18.5_mut3_cell35


title: E18.5_mut3_cell34


title: E18.5_mut3_cell32


title: E18.5_mut3_cell31


title: E18.5_mut3_cell29


title: E18.5_mut3_cell30


title: E18.5_mut3_cell50


title: E18.5_mut3_cell33


title: E18.5_mut3_cell26


title: E18.5_mut3_cell24


title: E18.5_mut3_cell27


title: E18.5_mut3_cell25


title: E18.5_mut3_cell23


title: E18.5_mut3_cell18


title: E18.5_mut3_cell22


title: E18.5_mut3_cell17


title: E18.5_mut3_cell20


title: E18.5_mut3_cell21


title: E18.5_mut3_cell19


title: E18.5_mut3_cell13


title: E18.5_mut3_cell14


title: E18.5_mut3_cell15


title: E18.5_mut3_cell11


title: E18.5_mut3_cell9


title: E18.5_mut3_cell28


title: E18.5_mut3_cell12


title: E18.5_mut3_cell10


title: E18.5_mut3_cell7


title: E18.5_mut3_cell4


title: E18.5_ctrl3_cell128

value: SstCre::RCE::Sox6 flox/+


title: E18.5_mut3_cell3


title: E18.5_mut3_cell1


title: E18.5_mut3_cell2


title: E18.5_mut3_cell6


title: E18.5_ctrl3_cell125


title: E18.5_ctrl3_cell126


title: E18.5_ctrl3_cell127


title: E18.5_ctrl3_cell122


title: E18.5_ctrl3_cell124


title: E18.5_ctrl3_cell123


title: E18.5_ctrl3_cell119


title: E18.5_ctrl3_cell120


title: E18.5_mut3_cell16


title: E18.5_ctrl3_cell118


title: E18.5_ctrl3_cell117


title: E18.5_ctrl3_cell121


title: E18.5_mut3_cell8


title: E18.5_ctrl3_cell115


title: E18.5_ctrl3_cell116


title: E18.5_ctrl3_cell113


title: E18.5_ctrl3_cell114


title: E18.5_mut3_cell5


title: E18.5_ctrl3_cell112


title: E18.5_ctrl3_cell111


title: E18.5_ctrl3_cell110


title: E18.5_ctrl3_cell108


title: E18.5_ctrl3_cell106


title: E18.5_ctrl3_cell102


title: E18.5_ctrl3_cell107


title: E18.5_ctrl3_cell101


title: E18.5_ctrl3_cell103


title: E18.5_ctrl3_cell104


title: E18.5_ctrl3_cell105


title: E18.5_ctrl3_cell100


title: E18.5_ctrl3_cell99


title: E18.5_ctrl3_cell98


title: E18.5_ctrl3_cell92


title: E18.5_ctrl3_cell95


title: E18.5_ctrl3_cell93


title: E18.5_ctrl3_cell96


title: E18.5_ctrl3_cell90


title: E18.5_ctrl3_cell91


title: E18.5_ctrl3_cell89


title: E18.5_ctrl3_cell109


title: E18.5_ctrl3_cell86


title: E18.5_ctrl3_cell84


title: E18.5_ctrl3_cell87


title: E18.5_ctrl3_cell83


title: E18.5_ctrl3_cell82


title: E18.5_ctrl3_cell85


title: E18.5_ctrl3_cell88


title: E18.5_ctrl3_cell79


title: E18.5_ctrl3_cell80


title: E18.5_ctrl3_cell81


title: E18.5_ctrl3_cell97


title: E18.5_ctrl3_cell73


title: E18.5_ctrl3_cell75


title: E18.5_ctrl3_cell94


title: E18.5_ctrl3_cell72


title: E18.5_ctrl3_cell76


title: E18.5_ctrl3_cell78


title: E18.5_ctrl3_cell77


title: E18.5_ctrl3_cell71


title: E18.5_ctrl3_cell74


title: E18.5_ctrl3_cell70


title: E18.5_ctrl3_cell68


title: E18.5_ctrl3_cell67


title: E18.5_ctrl3_cell66


title: E18.5_ctrl3_cell64


title: E18.5_ctrl3_cell65


title: E18.5_ctrl3_cell62


title: E18.5_ctrl3_cell63


title: E18.5_ctrl3_cell61


title: E18.5_ctrl3_cell58


title: E18.5_ctrl3_cell60


title: E18.5_ctrl3_cell57


title: E18.5_ctrl3_cell55


title: E18.5_ctrl3_cell54


title: E18.5_ctrl3_cell52


title: E18.5_ctrl3_cell53


title: E18.5_ctrl3_cell51


title: E18.5_ctrl3_cell69


title: E18.5_ctrl3_cell48


title: E18.5_ctrl3_cell50


title: E18.5_ctrl3_cell47


title: E18.5_ctrl3_cell49


title: E18.5_ctrl3_cell46


title: E14, dAT2, primed, replicate 2, CUT-RUN, Med1

city: Houston

first: Junwoo

last: Lee

state: Texas

address: 2120 El Paseo Street, Apt.603

department: Epigenetics and Molecular Carcinogenesis

country: USA

institute: MD Anderson Cancer Center

library_source: genomic

data_processing:
Adaptor trimming and low-quality reads were removed by Cutadapt.
The Reads were aligned to mm10 using Bowtie 2 alignment tool using --very-sensitive-local preset parameter.
Each sample was normalized using 1million reads from E. coli spikein control. Data from two biological replicates were first compared (R2 > 0.9), and then merged into a single read file for each time point.
Cut-Run peaks were then called using SEACR64 with ‘stringent’ ‘non’ ‘EFDR 0.01’ options in each sample.
Peaks were annotated using the ‘annotatePeaks’ module of HOMER package.
Assembly: mm10, M22
Supplementary files format and content: bw files normalized by spike-in control
Library strategy: CUT&RUN

molecule: genomic DNA

growth_protocol: Mouse embryonic stem cells (E14Tg2a, ATCC) were maintained on 1% gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore). Embryonic stem cells (ESCs) were cultured on gelatin-coated plates in DMEM (Invitrogen) supplemented with 15% FBS, 1X-Gultamax (Gibco), Na-Pyruvate (Gibco), 10mM 2-mercaptoethanol, 0.1 mM nonessential amino acids (Gibco), 1U/ml of ESGRO mLIF (Millipore), and 2i inhibitors (MEK inhibitor PD0325901, Gsk3b inhibitor (CHIR99021 – Stem Cell technology) in naïve (or +2i) condition. In epiblast stem cells (EpiSCs)  or primed condition, cells were cultured in chemically defined medium (IMDM and F12-Invitrogen) supplemented with 2%-BSA (Sigma), Insulin (Roche), Transferrin (Roche), CD-lipid concentrate (Gibco), FGF2 (R&D), and Activin-A (R&D).

extract_protocol:
CUT-RUN for Brg1, H3K27ac and Med1 in E14 WT and mutant ES cells was done using CUTANA ChIC/CUT&RUN kit (Epicypher #14-1048) following manufacturer’s protocol. Briefly, 5 × 10^5 cells were captured with Concanavalin A, permeabilized using 0.01% digitonin and incubated with 0.5 μg antibody (anti-Brg1 [#13-2002; Epicypher] / anti-H3K27ac [#13-0045; Epicypher]/ anti-Med1 [#17-10530; Millipore]) in 50 μL antibody buffer (20 mM HEPES at pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x protease inhibitor cocktails [EDTA-free tablet; Roche], 2 mM EDTA, 0.01% digitonin) for overnight. After removing unbound antibody, pAG-MNase (20X) in 50 μL cell permeabilization buffer was added to the cells and incubated for 10 min at RT. Then CaCl2 (2 mM) was added to activate MNase and incubated at 4 °C for 2 hr. The reaction was stopped using 33 μL of 2X STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 µg/mL RNase A, 50 µg/mL glycogen) and E. coli spike-in DNA (0.5ng) added as a control. The DNA from the released chromatin in the supernatant was purified and then quantified using Qubit dsDNA HS assay kit (Agilent Technologies).
CUT-RUN libraries were constructed using NEBNext Ultra II DNA library preparation kit. Briefly, end repair and dA-tailing were conducted on 6 ng of CUT&RUN eluted DNA for 30 min at 20°C followed by 30 min at 65°C. After adaptor ligation for 30 min at 20°C, the DNA fragments were purified by 1X vol of AMPure XP beads (Beckman Coulter) followed by 10-12 cycles of PCR amplification with Next Ultra II Q5 master mix. The PCR products were purified with 1X vol of AMPure XP beads.
These CUT-RUN libraries were submitted for sequencing (75bp paired end) on an Illumina HiSeq3000.

tag: cell line

value: embryonic stem cells

value: dAT

tag: treatment

value: FGF2 (R&D), and Activin-A (R&D)

tag: developmental stage

value: primed

tag: ip antibody

value: anti-Med1 [#17-10530; Millipore]


title: E14, dAT2, primed, replicate 1, CUT-RUN, Med1


title: E14, dAT1, primed, replicate 1, CUT-RUN, Med1


title: E14, dAT1, primed, replicate 2, CUT-RUN, Med1


title: E18.5_ctrl3_cell45


title: E18.5_ctrl3_cell43


title: E18.5_ctrl3_cell44


title: E14, dAT2, naïve, replicate 2, CUT-RUN, Med1

value: 2i inhibitors (MEK inhibitor PD0325901, Gsk3b inhibitor (CHIR99021 – Stem Cell technology))

value: naive


title: E18.5_ctrl3_cell41


title: E14, WT, primed, replicate 1, CUT-RUN, Med1


title: E14, dAT2, naïve, replicate 1, CUT-RUN, Med1


title: E18.5_ctrl3_cell59


title: E18.5_ctrl3_cell56


title: E18.5_ctrl3_cell42


title: E18.5_ctrl3_cell40


title: E18.5_ctrl3_cell39


title: E18.5_ctrl3_cell38


title: E14, dAT1, naïve, replicate 2, CUT-RUN, Med1

value: WT


title: E14, dAT1, naïve, replicate 1, CUT-RUN, Med1


title: E14, WT, naïve, replicate 1, CUT-RUN, Med1


title: E14, WT, naïve, replicate 2, CUT-RUN, Med1


title: E18.5_ctrl3_cell37

value: Neocortex


title: E14, dAT2, primed, replicate 1, CUT-RUN, H3K27ac

value: anti-H3K27ac [#13-0045; Epicypher]


title: E18.5_ctrl3_cell36

value: Somatostatin interneuron


title: E14, WT, primed, replicate 2, CUT-RUN, Med1


title: E18.5_ctrl3_cell35


title: E18.5_ctrl3_cell34


title: E14, dAT1, primed, replicate 1, CUT-RUN, H3K27ac


title: E14, dAT1, primed, replicate 2, CUT-RUN, H3K27ac


title: E18.5_ctrl3_cell32


title: E14, WT, primed, replicate 2, CUT-RUN, H3K27ac


title: E18.5_ctrl3_cell33


title: E18.5_ctrl3_cell31


title: E14, dAT2, naïve, replicate 2, CUT-RUN, H3K27ac


title: E18.5_ctrl3_cell28


title: E18.5_ctrl3_cell29


title: E14, dAT1, naïve, replicate 2, CUT-RUN, H3K27ac


title: E18.5_ctrl3_cell30


title: E14, dAT2, naïve, replicate 1, CUT-RUN, H3K27ac


title: E18.5_ctrl3_cell27


title: E14, dAT1, naïve, replicate 1, CUT-RUN, H3K27ac


title: E14, WT, naïve, replicate 2, CUT-RUN, H3K27ac


title: E18.5_ctrl3_cell26


title: E18.5_ctrl3_cell24


title: E18.5_ctrl3_cell25


title: E14, dAT2, primed, replicate 1, CUT-RUN, Brg1

value: anti-Brg1 [#13-2002; Epicypher]


title: E14, dAT2, primed, replicate 2, CUT-RUN, Brg1


title: E14, WT, naïve, replicate 1, CUT-RUN, H3K27ac


title: E14, dAT2, primed, replicate 2, CUT-RUN, H3K27ac


title: E18.5_ctrl3_cell23


title: E14, dAT1, primed, replicate 1, CUT-RUN, Brg1


title: E14, dAT1, primed, replicate 2, CUT-RUN, Brg1


title: E18.5_ctrl3_cell21


title: E14, WT, primed, replicate 1, CUT-RUN, H3K27ac


title: E14, WT, primed, replicate 2, CUT-RUN, Brg1


title: E14, WT, primed, replicate 1, CUT-RUN, Brg1


title: E18.5_ctrl3_cell20


title: E18.5_ctrl3_cell22


title: E14, dAT2, naïve, replicate 1, CUT-RUN, Brg1


title: E18.5_ctrl3_cell19


title: E18.5_ctrl3_cell18


title: E14, dAT1, naïve, replicate 2, CUT-RUN, Brg1


title: E14, dAT2, naïve, replicate 2, CUT-RUN, Brg1


title: E18.5_ctrl3_cell16


title: E14, dAT1, naïve, replicate 1, CUT-RUN, Brg1


title: E14, WT, naïve, replicate 1, CUT-RUN, Brg1


title: E14, dAT2, primed, replicate 2, CUT-RUN, IgG

description:
D8_CDM_H3K4me1_norm.bw
D8_CDM_MLL34.norm.bw

data_processing:
Adaptor trimming and low-quality reads were removed by Cutadapt.
The Reads were aligned to mm10 using Bowtie 2 alignment tool using --very-sensitive-local preset parameter.
Each sample was normalized using 1million reads from E. coli spikein control. Data from two biological replicates were first compared (R2 > 0.9), and then merged into a single read file for each time point.
Cut-Run peaks were then called using SEACR64 with ‘stringent’ ‘non’ ‘EFDR 0.01’ options in each sample.
Peaks were annotated using the ‘annotatePeaks’ module of HOMER package.
Assembly: mm10, M22
Supplementary files format and content: bw files normalized by spike-in control
Library strategy: CUT&Run

extract_protocol:
CUT-RUN for MLL3/4 and H3K4me1 in E14 WT and mutant ES cells was done using CUTANA ChIC/CUT&RUN kit (Epicypher #14-1048) following manufacturer’s protocol. Briefly, 5 × 105 cells were captured with Concanavalin A, permeabilized using 0.01% digitonin and incubated with 0.5 μg antibody (anti-MLL3/4 serum [kind gift from Dr. Joanna Wysocka] / anti-H3K4me1 [# 13-0040; Epicypher]/ IgG [# 13-0042; Epicypher]) in 50 μL antibody buffer (20 mM HEPES at pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x protease inhibitor cocktails [EDTA-free tablet; Roche], 2 mM EDTA, 0.01% digitonin) for overnight. After removing unbound antibody, pAG-MNase (20X) in 50 μL cell permeabilization buffer was added to the cells and incubated for 10 min at RT. Then CaCl2 (2 mM) was added to activate MNase and incubated at 4 °C for 2 hr. The reaction was stopped using 33 μL of 2X STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 µg/mL RNase A, 50 µg/mL glycogen) and E. coli spike-in DNA (0.5ng) added as a control. The DNA from the released chromatin in the supernatant was purified and then quantified using Qubit dsDNA HS assay kit (Agilent Technologies).
CUT-RUN libraries were constructed using NEBNext Ultra II DNA library preparation kit. Briefly, end repair and dA-tailing were conducted on 6 ng of CUT&RUN eluted DNA for 30 min at 20°C followed by 30 min at 65°C. After adaptor ligation for 30 min at 20°C, the DNA fragments were purified by 1X vol of AMPure XP beads (Beckman Coulter) followed by 10-12 cycles of PCR amplification with Next Ultra II Q5 master mix. The PCR products were purified with 1X vol of AMPure XP beads.

value: IgG (# 13-0042; Epicypher)


title: E14, WT, naïve, replicate 2, CUT-RUN, Brg1


title: E18.5_ctrl3_cell14


title: E18.5_ctrl3_cell13


title: E18.5_ctrl3_cell12


title: E18.5_ctrl3_cell11


title: E14, dAT2, naïve, replicate 2, CUT-RUN, IgG

description:
D8_2i_H3K4me1_norm.bw
D8_2i_MLL34.norm.bw


title: E18.5_ctrl3_cell9


title: E14, dAT2, naïve, replicate 1, CUT-RUN, IgG


title: E18.5_ctrl3_cell10


title: E18.5_ctrl3_cell8


title: E14, dAT2, primed, replicate 1, CUT-RUN, IgG


title: E14, dAT1, primed, replicate 2, CUT-RUN, IgG

description:
A2_CDM_H3K4me1_norm.bw
A2_CDM_MLL34.norm.bw


title: E18.5_ctrl3_cell7


title: E18.5_ctrl3_cell17


title: E14, dAT1, naïve, replicate 2, CUT-RUN, IgG

description:
A2_2i_H3K4me1_norm.bw
A2_2i_MLL34.norm.bw


title: E18.5_ctrl3_cell3


title: E18.5_ctrl3_cell4


title: E14, WT, primed, replicate 2, CUT-RUN, IgG

description:
WT_CDM_H3K4me1_norm.bw
WT_CDM_MLL34.norm.bw


title: E18.5_ctrl3_cell15


title: E14, dAT1, naïve, replicate 1, CUT-RUN, IgG


title: E18.5_ctrl3_cell6


title: E18.5_ctrl3_cell2


title: E14, WT, naïve, replicate 2, CUT-RUN, IgG

description:
WT_2i_H3K4me1_norm.bw
WT_2i_MLL34.norm.bw


title: E14, WT, primed, replicate 1, CUT-RUN, IgG


title: E14, dAT2, primed, replicate 2, CUT-RUN, MLL34

value: MLL34 (serum; kind gift from Dr. Joanna Wysocka)


title: E18.5_ctrl2_cell127


title: E14, dAT2, primed, replicate 1, CUT-RUN, MLL34


title: E14, dAT2, naïve, replicate 2, CUT-RUN, MLL34


title: E14, dAT1, primed, replicate 1, CUT-RUN, IgG


title: E18.5_ctrl3_cell5


title: E18.5_ctrl2_cell125


title: E14, dAT2, naïve, replicate 1, CUT-RUN, MLL34


title: E18.5_ctrl2_cell124


title: E14, dAT1, primed, replicate 2, CUT-RUN, MLL34


title: E18.5_ctrl2_cell126


title: E18.5_ctrl2_cell123


title: E14, WT, primed, replicate 2, CUT-RUN, MLL34


title: E18.5_ctrl2_cell120


title: E14, WT, naïve, replicate 1, CUT-RUN, MLL34


title: E18.5_ctrl2_cell118


title: E14, WT, primed, replicate 1, CUT-RUN, MLL34


title: E18.5_ctrl2_cell116


title: E18.5_ctrl2_cell121


title: E14, dAT1, primed, replicate 1, CUT-RUN, MLL34


title: E14, WT, naïve, replicate 1, CUT-RUN, IgG


title: E18.5_ctrl2_cell117


title: E14, dAT2, primed, replicate 2, CUT-RUN, H3K4me1


title: E18.5_ctrl2_cell119


title: E14, WT, naïve, replicate 2, CUT-RUN, MLL34


title: E18.5_ctrl3_cell1


title: E18.5_ctrl2_cell115


title: E14, dAT2, naïve, replicate 2, CUT-RUN, H3K4me1


title: E14, dAT2, primed, replicate 1, CUT-RUN, H3K4me1


title: E18.5_ctrl2_cell114


title: E14, dAT1, naïve, replicate 2, CUT-RUN, MLL34


title: E18.5_ctrl2_cell128


title: E18.5_ctrl2_cell122


title: E18.5_ctrl2_cell113


title: E14, dAT2, naïve, replicate 1, CUT-RUN, H3K4me1


title: E14, dAT1, primed, replicate 1, CUT-RUN, H3K4me1


title: E14, dAT1, primed, replicate 2, CUT-RUN, H3K4me1


title: E18.5_ctrl2_cell110


title: E18.5_ctrl2_cell112


title: E18.5_ctrl2_cell111


title: E18.5_ctrl2_cell109


title: E14, WT, naïve, replicate 1, CUT-RUN, H3K4me1


title: E14, dAT1, naïve, replicate 1, CUT-RUN, H3K4me1


title: E14, dAT1, naïve, replicate 2, CUT-RUN, H3K4me1


title: E14, WT, primed, replicate 2, CUT-RUN, H3K4me1


title: E18.5_ctrl2_cell107


title: E14, WT, naïve, replicate 2, CUT-RUN, H3K4me1


title: E18.5_ctrl2_cell106


title: E18.5_ctrl2_cell103


title: E18.5_ctrl2_cell105


title: E18.5_ctrl2_cell101


title: E18.5_ctrl2_cell102


title: E18.5_ctrl2_cell104


title: Rat kidney [148-2Input]

city: Guangzhou

first: Wei

last: Zhu

address: No.1 Kangda Road, Haizhu District, Guangzhou City, Guangdong Province

country: China

institute: The First Affiliated Hospital of Guangzhou Medical University

library_source: other

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.Genomic alignment (rn6) was using Tophat(version:2.0.13) to get uniquely mapping reads.
RIPseekre was employed to perform peak calling.Then using Hommer(version:4.8) to annotate the Peaks.The nucleotides in Peaks region were used for detection of the consensus motif by DREME (version: 4.11.1) and MEME(version:4.11.1). Motif central enrichment was performed by CentriMo (version:4.11.1). Differential peak enrichment was determined by Pyicoenrich(version:2.0.7).
Assembly: rn6
Supplementary files format and content: *.peaks.txt
Supplementary files format and content: *.peaksStat.txt
Supplementary files format and content: *.expression.txt

molecule: other

organism: Rattus norvegicus

source_name: kidney

extract_protocol:
RNA immunoprecipitation was performed using RIP Kit (Bersinbio, Guangzhou). The kidney lysates from rats were incubated with 5 μg Argonaute-2 (Ago2) antibody (ab186733, Abcam) or a control anti-immunoglobulin G (IgG) antibody (Abcam) coated beads at 4℃ overnight under rotation. The immunoprecipitates were eluted from the beads with elution buffer and the RNAs were purified. Then, purified RNAs were reverse-transcribed into complementary DNA (cDNA). The libraries were prepared according to the manufacturer’s instructions and sequenced on an Illumina HiSeqTM 2500 platform by Guangzhou RiboBio Co., Ltd.
Antibody immunoprecipitation RNA was quality control with QubitTM(Thermo Fisher Scientifc,USA) and Agilent 2200 TapeStation (Agilent Technologies, USA). Then, 100ng RNA was used for library building following NEBNext® Ultra™ RNA Library Prep Kit protocol for Illumina (NEB, USA). The final library product was assessed with Agilent 2200 TapeStation andQubit®2.0(Life Technologies, USA)

value: kidney


title: RNAi_ARES_D

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

country: France

institute: CNRS

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed using trimmomatic V0.36 to remove adapters and low quality bases. Ribosomal RNA where removed using SortMeRNA (v2.1)
trimmed reads were aligned to the TAIR10 genome using STAR (2.7.2a)
Reads were counted on each Araport11 features using featureCounts from subreads package (v1.6.5) using strand specific mode (-s 2 -O -M –fraction).
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Media = MS/2, pH 5.8, Temperature = 21°C day/ 21°c night Light = 16 hours day / 8 hours night for 12 days.

extract_protocol:
Total RNA was isolated using QuickRNA Miniprep Kit from Zymo Research and treat with DNAse according to manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols using Stranded mRNA Prep kit

value: root

tag: ecotype

value: RNAi ARES


title: E18.5_ctrl2_cell100

value: SstCre::RCE::Sox6 flox/+


title: E18.5_ctrl2_cell108


title: E18.5_ctrl2_cell99


title: E14, WT, primed, replicate 1, CUT-RUN, H3K4me1

value: embryonic stem cells


title: RNAi_ARES_C


title: E18.5_ctrl2_cell98


title: Rat kidney [148-2IP]


title: E18.5_ctrl2_cell97


title: Rat kidney [CK-4IP]


title: Col0 D

value: wild type


title: E18.5_ctrl2_cell96


title: Rat kidney [CK-4Input]


title: RNAi_ARES_A


title: E18.5_ctrl2_cell93


title: RNAi_ARES_B


title: E18.5_ctrl2_cell95


title: Col0 B


title: E18.5_ctrl2_cell94


title: Col0 A


title: Col0 C


title: E18.5_ctrl2_cell92


title: P21-28_ctrl_Pvalb75

description:
C1-STRT
Munguba_Nikouei_P21to28_PvalbCells_counts.txt
Munguba_Nikouei_P21to28_PvalbCells_annotation.txt

data_processing:
Data processing acccording to (Islam et al., 2014; DOI: 10.1038/nmeth.2772) and  (Zeisel et al. 2015;  DOI: 10.1126/science.aaa1934).
genome build: mm10
Tab-delimited text format, in which cells make up the columns and genes the rows, with corresponding cell annotation file.

source_name: Primary somatosensory cortex

extract_protocol:
At postnatal day 21-28 (P21-28) the animals were anesthetized with ketamine/xylazine (4:1), then transcardially perfused with cutting solution of the following composition (in mM): 87 NaCl, 75 sucrose, 2.5 KCl, 25 NaHCO3, 1.25 NaH2PO4, 7 MgCl2, 1 CaCl2, and 10 glucose. The brains were quickly removed and transferred to ice-cold cutting-solution, subsequently fixed to a stage and 300 μm brain slices were cut on a vibratome (VT1200 S, Leica). Tissue corresponding to primary somatosensory cortex (S1) was dissected and dissociated into a single cell suspension, as previously described (Muñoz-Manchado et al. 2018; DOI: 10.1016/j.celrep.2018.07.053). Briefly, the tissue was dissociated using the Papain dissociation system (Worthington) following the manufacturer’s instructions. Cell suspension obtained was filtered with 20 μm filter (Partec) and kept in cold oxygenated Hank's balanced buffer solution (HBSS; Sigma) with 0.2% bovine serum albumin (BSA) and 0.3% glucose. Cells were sorted based on fluorescence (eGFP or tdTomato), and then loaded on the Fluidigm C1 platform, where they were processed according to the C1-STRT protocol (Zeisel et al. 2015;  DOI: 10.1126/science.aaa1934); including imaging, high-throughput sequencing (Illumina) and molecule counting (UMI). Visual doublets were excluded, and only fluorescent single cells were processed for RNA sequencing.
The libraries were generated according to the C1-STRT protocol (Islam et al., 2014; DOI: 10.1038/nmeth.2772).

value: Primary somatosensory cortex

value: Parvalbumin interneuron

value: PvalbCre::RCE::Sox6 +/+


title: P21-28_ctrl_Pvalb73


title: P21-28_ctrl_Pvalb74


title: E14, dAT1, naïve, replicate 1, CUT-RUN, MLL34

value: dAT

value: 2i inhibitors (MEK inhibitor PD0325901, Gsk3b inhibitor (CHIR99021 – Stem Cell technology))

value: naive


title: E18.5_ctrl2_cell90

value: Neocortex


title: P21-28_ctrl_Pvalb72


title: E18.5_ctrl2_cell88

value: Somatostatin interneuron


title: E18.5_ctrl2_cell87


title: P21-28_ctrl_Pvalb69


title: P21-28_ctrl_Pvalb71


title: E18.5_ctrl2_cell91


title: P21-28_ctrl_Pvalb70


title: E18.5_ctrl2_cell85


title: P21-28_ctrl_Pvalb65


title: P21-28_ctrl_Pvalb68


title: E18.5_ctrl2_cell84


title: E18.5_ctrl2_cell86


title: E18.5_ctrl2_cell82


title: P21-28_ctrl_Pvalb67


title: E18.5_ctrl2_cell83


title: E18.5_ctrl2_cell80


title: E18.5_ctrl2_cell81


title: E18.5_ctrl2_cell79


title: P21-28_ctrl_Pvalb66


title: E18.5_ctrl2_cell77


title: E18.5_ctrl2_cell76


title: P21-28_ctrl_Pvalb60


title: P21-28_ctrl_Pvalb63


title: E18.5_ctrl2_cell89


title: E18.5_ctrl2_cell78


title: P21-28_ctrl_Pvalb57


title: E18.5_ctrl2_cell75


title: E18.5_ctrl2_cell74


title: P21-28_ctrl_Pvalb58


title: P21-28_ctrl_Pvalb59


title: P21-28_ctrl_Pvalb56


title: P21-28_ctrl_Pvalb64


title: P21-28_ctrl_Pvalb55


title: E18.5_ctrl2_cell73


title: E18.5_ctrl2_cell72


title: E18.5_ctrl2_cell71


title: P21-28_ctrl_Pvalb53


title: P21-28_ctrl_Pvalb62


title: E18.5_ctrl2_cell70


title: P21-28_ctrl_Pvalb52


title: P21-28_ctrl_Pvalb54


title: E18.5_ctrl2_cell68


title: P21-28_ctrl_Pvalb50


title: P21-28_ctrl_Pvalb51


title: E18.5_ctrl2_cell67


title: E18.5_ctrl2_cell66


title: P21-28_ctrl_Pvalb49


title: E18.5_ctrl2_cell65


title: P21-28_ctrl_Pvalb48


title: E18.5_ctrl2_cell63


title: E18.5_ctrl2_cell64


title: P21-28_ctrl_Pvalb46


title: P21-28_ctrl_Pvalb47


title: P21-28_ctrl_Pvalb45


title: E18.5_ctrl2_cell62


title: P21-28_ctrl_Pvalb44


title: P21-28_ctrl_Pvalb43


title: E18.5_ctrl2_cell60


title: P21-28_ctrl_Pvalb42


title: P21-28_ctrl_Pvalb41


title: E18.5_ctrl2_cell69


title: E18.5_ctrl2_cell59


title: P21-28_ctrl_Pvalb40


title: E18.5_ctrl2_cell56


title: E18.5_ctrl2_cell58


title: P21-28_ctrl_Pvalb39


title: E18.5_ctrl2_cell54


title: E18.5_ctrl2_cell55


title: E18.5_ctrl2_cell53


title: P21-28_ctrl_Pvalb37


title: P21-28_ctrl_Pvalb38


title: P21-28_ctrl_Pvalb36


title: P21-28_ctrl_Pvalb61


title: E18.5_ctrl2_cell52


title: E18.5_ctrl2_cell51


title: P21-28_ctrl_Pvalb34


title: E18.5_ctrl2_cell61


title: E18.5_ctrl2_cell50


title: P21-28_ctrl_Pvalb33


title: E18.5_ctrl2_cell48


title: E18.5_ctrl2_cell49


title: P21-28_ctrl_Pvalb31


title: P21-28_ctrl_Pvalb30


title: P21-28_ctrl_Pvalb32


title: E18.5_ctrl2_cell46


title: E18.5_ctrl2_cell47


title: E18.5_ctrl2_cell45


title: P21-28_ctrl_Pvalb29


title: P21-28_ctrl_Pvalb28


title: E18.5_ctrl2_cell57


title: P21-28_ctrl_Pvalb27


title: E18.5_ctrl2_cell44


title: P21-28_ctrl_Pvalb26


title: P21-28_ctrl_Pvalb25


title: E18.5_ctrl2_cell43


title: P21-28_ctrl_Pvalb35


title: E18.5_ctrl2_cell41


title: E18.5_ctrl2_cell42


title: E18.5_ctrl2_cell39


title: P21-28_ctrl_Pvalb24


title: P21-28_ctrl_Pvalb23


title: P21-28_ctrl_Pvalb22


title: E18.5_ctrl2_cell38


title: E18.5_ctrl2_cell40


title: P21-28_ctrl_Pvalb20


title: E18.5_ctrl2_cell37


title: P21-28_ctrl_Pvalb17


title: P21-28_ctrl_Pvalb19


title: E18.5_ctrl2_cell34


title: P21-28_ctrl_Pvalb16


title: E18.5_ctrl2_cell35


title: P21-28_ctrl_Pvalb15


title: E18.5_ctrl2_cell33


title: P21-28_ctrl_Pvalb14


title: P21-28_ctrl_Pvalb13


title: P21-28_ctrl_Pvalb21


title: E18.5_ctrl2_cell31


title: P21-28_ctrl_Pvalb12


title: P21-28_ctrl_Pvalb11


title: E18.5_ctrl2_cell29


title: E18.5_ctrl2_cell32


title: E18.5_ctrl2_cell28


title: E18.5_ctrl2_cell30


title: E18.5_ctrl2_cell27


title: E18.5_ctrl2_cell26


title: E18.5_ctrl2_cell36


title: P21-28_ctrl_Pvalb10


title: P21-28_ctrl_Pvalb18


title: P21-28_ctrl_Pvalb9


title: P21-28_ctrl_Pvalb8


title: P21-28_ctrl_Pvalb6


title: E18.5_ctrl2_cell25


title: E18.5_ctrl2_cell23


title: P21-28_ctrl_Pvalb5


title: E18.5_ctrl2_cell22


title: P21-28_ctrl_Pvalb4


title: E18.5_ctrl2_cell21


title: E18.5_ctrl2_cell20


title: P21-28_ctrl_Pvalb2


title: P21-28_ctrl_Pvalb3


title: P21-28_ctrl_Pvalb1


title: P21-28_mut_Sst78

description:
C1-STRT
Munguba_Nikouei_P21to28_SstCells_counts.txt
Munguba_Nikouei_P21to28_SstCells_annotation.txt

value: SstCre::RCE::Sox6 flox/-


title: E18.5_ctrl2_cell17


title: P21-28_mut_Sst77


title: P21-28_mut_Sst75


title: P21-28_mut_Sst79


title: P21-28_mut_Sst76


title: E18.5_ctrl2_cell24


title: E18.5_ctrl2_cell14


title: P21-28_mut_Sst74


title: E18.5_ctrl2_cell15


title: P21-28_mut_Sst73


title: E18.5_ctrl2_cell12


title: E18.5_ctrl2_cell19


title: E18.5_ctrl2_cell16


title: E18.5_ctrl2_cell18


title: E18.5_ctrl2_cell11


title: P21-28_mut_Sst70


title: P21-28_mut_Sst71


title: P21-28_ctrl_Pvalb7


title: E18.5_ctrl2_cell10


title: E18.5_ctrl2_cell13


title: E18.5_ctrl2_cell8


title: P21-28_mut_Sst69


title: E18.5_ctrl2_cell9


title: E18.5_ctrl2_cell7


title: P21-28_mut_Sst68


title: E18.5_ctrl2_cell6


title: E18.5_ctrl2_cell5


title: P21-28_mut_Sst67


title: P21-28_mut_Sst72


title: P21-28_mut_Sst64


title: P21-28_mut_Sst63


title: E18.5_ctrl2_cell3


title: P21-28_mut_Sst66


title: E18.5_mut2_cell125

value: SstCre::RCE::Sox6 flox/flox


title: P21-28_mut_Sst59


title: P21-28_mut_Sst60


title: P21-28_mut_Sst65


title: P21-28_mut_Sst62


title: E18.5_ctrl2_cell4


title: E18.5_mut2_cell121


title: P21-28_mut_Sst61


title: E18.5_ctrl2_cell2


title: E18.5_ctrl2_cell1


title: E18.5_mut2_cell124


title: E18.5_mut2_cell126


title: P21-28_mut_Sst56


title: E18.5_mut2_cell120


title: P21-28_mut_Sst58


title: P21-28_mut_Sst55


title: P21-28_mut_Sst57


title: E18.5_mut2_cell119


title: P21-28_mut_Sst54


title: E18.5_mut2_cell118


title: P21-28_mut_Sst53


title: E18.5_mut2_cell123


title: E18.5_mut2_cell117


title: P21-28_mut_Sst52


title: E18.5_mut2_cell122


title: E18.5_mut2_cell116


title: E18.5_mut2_cell115


title: P21-28_mut_Sst49


title: P21-28_mut_Sst50


title: P21-28_mut_Sst51


title: P21-28_mut_Sst47


title: E18.5_mut2_cell114


title: E18.5_mut2_cell111


title: P21-28_mut_Sst46


title: P21-28_mut_Sst44


title: E18.5_mut2_cell112


title: E18.5_mut2_cell113


title: E18.5_mut2_cell107


title: E18.5_mut2_cell108


title: P21-28_mut_Sst48


title: E18.5_mut2_cell109


title: P21-28_mut_Sst45


title: E18.5_mut2_cell110


title: P21-28_mut_Sst42


title: P21-28_mut_Sst43


title: E18.5_mut2_cell106


title: P21-28_mut_Sst41


title: P21-28_mut_Sst39


title: E18.5_mut2_cell103


title: P21-28_mut_Sst38


title: E18.5_mut2_cell102


title: P21-28_mut_Sst37


title: E18.5_mut2_cell101


title: P21-28_mut_Sst36


title: E18.5_mut2_cell105


title: E18.5_mut2_cell100


title: P21-28_mut_Sst40


title: E18.5_mut2_cell98


title: P21-28_mut_Sst34


title: E18.5_mut2_cell99


title: P21-28_mut_Sst31


title: P21-28_mut_Sst29


title: P21-28_mut_Sst30


title: P21-28_mut_Sst28


title: E18.5_mut2_cell104


title: E18.5_mut2_cell92


title: P21-28_mut_Sst32


title: P21-28_mut_Sst33


title: P21-28_mut_Sst27


title: E18.5_mut2_cell93


title: E18.5_mut2_cell94


title: P21-28_mut_Sst26


title: P21-28_mut_Sst25


title: E18.5_mut2_cell89


title: P21-28_mut_Sst24


title: E18.5_mut2_cell88


title: P21-28_mut_Sst23


title: P21-28_mut_Sst35


title: E18.5_mut2_cell96


title: E18.5_mut2_cell87


title: E18.5_mut2_cell95


title: P21-28_mut_Sst22


title: E18.5_mut2_cell86


title: P21-28_mut_Sst21


title: E18.5_mut2_cell85


title: E18.5_mut2_cell91


title: P21-28_mut_Sst20


title: P21-28_mut_Sst19


title: E18.5_mut2_cell79


title: P21-28_mut_Sst16


title: P21-28_mut_Sst14


title: P21-28_mut_Sst18


title: P21-28_mut_Sst17


title: E18.5_mut2_cell82


title: E18.5_mut2_cell83


title: P21-28_mut_Sst15


title: E18.5_mut2_cell90


title: E18.5_mut2_cell81


title: E18.5_mut2_cell84


title: E18.5_mut2_cell78


title: P21-28_mut_Sst12


title: P21-28_mut_Sst13


title: E18.5_mut2_cell76


title: P21-28_mut_Sst11


title: E18.5_mut2_cell75


title: E18.5_mut2_cell97


title: P21-28_mut_Sst10


title: E18.5_mut2_cell74


title: P21-28_mut_Sst9


title: E18.5_mut2_cell73


title: E18.5_mut2_cell72


title: P21-28_mut_Sst8


title: E18.5_mut2_cell80


title: E18.5_mut2_cell71


title: P21-28_mut_Sst6


title: E18.5_mut2_cell70


title: E18.5_mut2_cell77


title: E18.5_mut2_cell69


title: P21-28_mut_Sst2


title: E18.5_mut2_cell65


title: E18.5_mut2_cell66


title: E18.5_mut2_cell68


title: P21-28_mut_Sst3


title: P21-28_mut_Sst4


title: E18.5_mut2_cell63


title: E18.5_mut2_cell67


title: P21-28_ctrl_Sst256


title: P21-28_ctrl_Sst255


title: E18.5_mut2_cell64


title: P21-28_mut_Sst1


title: P21-28_ctrl_Sst254


title: P21-28_ctrl_Sst253


title: E18.5_mut2_cell62


title: P21-28_ctrl_Sst252


title: P21-28_mut_Sst7


title: E18.5_mut2_cell60


title: E18.5_mut2_cell59


title: E18.5_mut2_cell58


title: P21-28_ctrl_Sst251


title: E18.5_mut2_cell57


title: P21-28_ctrl_Sst250


title: P21-28_ctrl_Sst249


title: P21-28_ctrl_Sst248


title: P21-28_mut_Sst5


title: E18.5_mut2_cell56


title: P21-28_ctrl_Sst247


title: E18.5_mut2_cell55


title: E18.5_mut2_cell53


title: E18.5_mut2_cell54


title: E18.5_mut2_cell61


title: P21-28_ctrl_Sst243


title: E18.5_mut2_cell52


title: P21-28_ctrl_Sst245


title: E18.5_mut2_cell51


title: P21-28_ctrl_Sst244


title: E18.5_mut2_cell48


title: P21-28_ctrl_Sst239


title: P21-28_ctrl_Sst242


title: P21-28_ctrl_Sst240


title: P21-28_ctrl_Sst241


title: E18.5_mut2_cell49


title: E18.5_mut2_cell47


title: P21-28_ctrl_Sst237


title: P21-28_ctrl_Sst238


title: E18.5_mut2_cell46


title: E18.5_mut2_cell45


title: E18.5_mut2_cell44


title: E18.5_mut2_cell43


title: P21-28_ctrl_Sst235


title: P21-28_ctrl_Sst233


title: P21-28_ctrl_Sst246


title: P21-28_ctrl_Sst236


title: E18.5_mut2_cell42


title: P21-28_ctrl_Sst234


title: E18.5_mut2_cell41


title: E18.5_mut2_cell50


title: E18.5_mut2_cell40


title: E18.5_mut2_cell39


title: P21-28_ctrl_Sst230


title: P21-28_ctrl_Sst231


title: E18.5_mut2_cell37


title: P21-28_ctrl_Sst228


title: P21-28_ctrl_Sst229


title: E18.5_mut2_cell36


title: E18.5_mut2_cell35


title: P21-28_ctrl_Sst227


title: E18.5_mut2_cell33


title: P21-28_ctrl_Sst224


title: E18.5_mut2_cell34


title: P21-28_ctrl_Sst226


title: E18.5_mut2_cell32


title: P21-28_ctrl_Sst225


title: E18.5_mut2_cell31


title: P21-28_ctrl_Sst223


title: E18.5_mut2_cell29


title: E18.5_mut2_cell30


title: E18.5_mut2_cell28


title: P21-28_ctrl_Sst232


title: P21-28_ctrl_Sst221


title: P21-28_ctrl_Sst220


title: E18.5_mut2_cell27


title: E18.5_mut2_cell38


title: P21-28_ctrl_Sst222


title: E18.5_mut2_cell25


title: P21-28_ctrl_Sst218


title: E18.5_mut2_cell26


title: P21-28_ctrl_Sst219


title: P21-28_ctrl_Sst216


title: P21-28_ctrl_Sst215


title: E18.5_mut2_cell21


title: E18.5_mut2_cell23


title: E18.5_mut2_cell22


title: P21-28_ctrl_Sst212


title: P21-28_ctrl_Sst211


title: E18.5_mut2_cell20


title: E18.5_mut2_cell19


title: E18.5_mut2_cell18


title: P21-28_ctrl_Sst213


title: E18.5_mut2_cell17


title: P21-28_ctrl_Sst210


title: P21-28_ctrl_Sst217


title: E18.5_mut2_cell16


title: P21-28_ctrl_Sst207


title: E18.5_mut2_cell15


title: P21-28_ctrl_Sst206


title: E18.5_mut2_cell14


title: P21-28_ctrl_Sst205


title: E18.5_mut2_cell13


title: E18.5_mut2_cell24


title: P21-28_ctrl_Sst214


title: P21-28_ctrl_Sst204


title: P21-28_ctrl_Sst203


title: E18.5_mut2_cell12


title: E18.5_mut2_cell11


title: E18.5_mut2_cell10


title: P21-28_ctrl_Sst202


title: P21-28_ctrl_Sst201


title: P21-28_ctrl_Sst209


title: P21-28_ctrl_Sst200


title: P21-28_ctrl_Sst199


title: E18.5_mut2_cell7


title: E18.5_mut2_cell9


title: E18.5_mut2_cell8


title: P21-28_ctrl_Sst197


title: E18.5_mut2_cell5


title: P21-28_ctrl_Sst208


title: E18.5_mut2_cell6


title: E18.5_mut2_cell4


title: P21-28_ctrl_Sst198


title: P21-28_ctrl_Sst195


title: P21-28_ctrl_Sst194


title: P21-28_ctrl_Sst196


title: P21-28_ctrl_Sst193


title: E18.5_mut2_cell3


title: E18.5_mut1_cell127


title: E18.5_mut2_cell2


title: E18.5_mut1_cell128


title: P21-28_ctrl_Sst191


title: P21-28_ctrl_Sst190


title: E18.5_mut1_cell126


title: E18.5_mut2_cell1


title: E18.5_mut1_cell125


title: P21-28_ctrl_Sst189


title: P21-28_ctrl_Sst188


title: E18.5_mut1_cell124


title: E18.5_mut1_cell123


title: P21-28_ctrl_Sst192


title: P21-28_ctrl_Sst186


title: P21-28_ctrl_Sst184


title: P21-28_ctrl_Sst185


title: E18.5_mut1_cell119


title: P21-28_ctrl_Sst181


title: P21-28_ctrl_Sst182


title: E18.5_mut1_cell121


title: E18.5_mut1_cell118


title: E18.5_mut1_cell122


title: E18.5_mut1_cell117


title: E18.5_mut1_cell120


title: E18.5_mut1_cell115


title: P21-28_ctrl_Sst180


title: P21-28_ctrl_Sst179


title: P21-28_ctrl_Sst187


title: E18.5_mut1_cell114


title: P21-28_ctrl_Sst177


title: E18.5_mut1_cell112


title: P21-28_ctrl_Sst178


title: E18.5_mut1_cell113


title: P21-28_ctrl_Sst175


title: E18.5_mut1_cell111


title: P21-28_ctrl_Sst176


title: P21-28_ctrl_Sst183


title: E18.5_mut1_cell109


title: E18.5_mut1_cell110


title: P21-28_ctrl_Sst172


title: P21-28_ctrl_Sst174


title: P21-28_ctrl_Sst173


title: E18.5_mut1_cell108


title: P21-28_ctrl_Sst171


title: P21-28_ctrl_Sst169


title: P21-28_ctrl_Sst170


title: E18.5_mut1_cell116


title: E18.5_mut1_cell106


title: P21-28_ctrl_Sst168


title: E18.5_mut1_cell104


title: E18.5_mut1_cell103


title: P21-28_ctrl_Sst167


title: E18.5_mut1_cell102


title: P21-28_ctrl_Sst166


title: E18.5_mut1_cell100


title: P21-28_ctrl_Sst161


title: P21-28_ctrl_Sst164


title: E18.5_mut1_cell99


title: P21-28_ctrl_Sst160


title: E18.5_mut1_cell107


title: E18.5_mut1_cell101


title: P21-28_ctrl_Sst165


title: E18.5_mut1_cell98


title: P21-28_ctrl_Sst157


title: P21-28_ctrl_Sst163


title: E18.5_mut1_cell97


title: P21-28_ctrl_Sst155


title: P21-28_ctrl_Sst162


title: E18.5_mut1_cell96


title: E18.5_mut1_cell92


title: E18.5_mut1_cell95


title: E18.5_mut1_cell94


title: E18.5_mut1_cell105


title: P21-28_ctrl_Sst158


title: E18.5_mut1_cell93


title: E18.5_mut1_cell91


title: P21-28_ctrl_Sst152


title: E18.5_mut1_cell88


title: P21-28_ctrl_Sst154


title: E18.5_mut1_cell87


title: P21-28_ctrl_Sst150


title: E18.5_mut1_cell85


title: P21-28_ctrl_Sst149


title: P21-28_ctrl_Sst147


title: P21-28_ctrl_Sst153


title: E18.5_mut1_cell90


title: E18.5_mut1_cell89


title: E18.5_mut1_cell83


title: P21-28_ctrl_Sst159


title: P21-28_ctrl_Sst146


title: E18.5_mut1_cell82


title: E18.5_mut1_cell86


title: E18.5_mut1_cell80


title: P21-28_ctrl_Sst145


title: P21-28_ctrl_Sst156


title: E18.5_mut1_cell84


title: P21-28_ctrl_Sst142


title: E18.5_mut1_cell81


title: E18.5_mut1_cell78


title: P21-28_ctrl_Sst144


title: P21-28_ctrl_Sst143


title: E18.5_mut1_cell79


title: E18.5_mut1_cell75


title: P21-28_ctrl_Sst139


title: E18.5_mut1_cell73


title: P21-28_ctrl_Sst136


title: P21-28_ctrl_Sst134


title: E18.5_mut1_cell76


title: E18.5_mut1_cell70


title: P21-28_ctrl_Sst151


title: E18.5_mut1_cell74


title: P21-28_ctrl_Sst140


title: P21-28_ctrl_Sst138


title: P21-28_ctrl_Sst141


title: P21-28_ctrl_Sst135


title: P21-28_ctrl_Sst148


title: P21-28_ctrl_Sst137


title: E18.5_mut1_cell72


title: E18.5_mut1_cell66


title: E18.5_mut1_cell68


title: P21-28_ctrl_Sst130


title: E18.5_mut1_cell69


title: P21-28_ctrl_Sst131


title: P21-28_ctrl_Sst133


title: P21-28_ctrl_Sst132


title: E18.5_mut1_cell65


title: E18.5_mut1_cell77


title: P21-28_ctrl_Sst128


title: E18.5_mut1_cell64


title: E18.5_mut1_cell63


title: P21-28_ctrl_Sst129


title: P21-28_ctrl_Sst127


title: E18.5_mut1_cell71


title: E18.5_mut1_cell62


title: P21-28_ctrl_Sst126


title: E18.5_mut1_cell61


title: P21-28_ctrl_Sst125


title: P21-28_ctrl_Sst124


title: E18.5_mut1_cell60


title: P21-28_ctrl_Sst123


title: P21-28_ctrl_Sst122


title: E18.5_mut1_cell67


title: P21-28_ctrl_Sst121


title: E18.5_mut1_cell57


title: P21-28_ctrl_Sst120


title: E18.5_mut1_cell55


title: P21-28_ctrl_Sst119


title: P21-28_ctrl_Sst118


title: E18.5_mut1_cell54


title: P21-28_ctrl_Sst116


title: E18.5_mut1_cell52


title: P21-28_ctrl_Sst115


title: E18.5_mut1_cell51


title: P21-28_ctrl_Sst117


title: P21-28_ctrl_Sst114


title: E18.5_mut1_cell50


title: E18.5_mut1_cell49


title: P21-28_ctrl_Sst113


title: P21-28_ctrl_Sst112


title: P21-28_ctrl_Sst111


title: E18.5_mut1_cell58


title: P21-28_ctrl_Sst110


title: E18.5_mut1_cell59


title: P21-28_ctrl_Sst108


title: P21-28_ctrl_Sst107


title: E18.5_mut1_cell44


title: E18.5_mut1_cell45


title: P21-28_ctrl_Sst109


title: E18.5_mut1_cell43


title: E18.5_mut1_cell56


title: P21-28_ctrl_Sst106


title: E18.5_mut1_cell42


title: E18.5_mut1_cell53


title: P21-28_ctrl_Sst105


title: E18.5_mut1_cell41


title: P21-28_ctrl_Sst104


title: P21-28_ctrl_Sst103


title: E18.5_mut1_cell39


title: E18.5_mut1_cell40


title: E18.5_mut1_cell38


title: P21-28_ctrl_Sst102


title: E18.5_mut1_cell48


title: P21-28_ctrl_Sst100


title: P21-28_ctrl_Sst99


title: P21-28_ctrl_Sst101


title: E18.5_mut1_cell47


title: E18.5_mut1_cell36


title: E18.5_mut1_cell35


title: E18.5_mut1_cell46


title: P21-28_ctrl_Sst97


title: P21-28_ctrl_Sst98


title: E18.5_mut1_cell33


title: E18.5_mut1_cell34


title: P21-28_ctrl_Sst96


title: E18.5_mut1_cell32


title: E18.5_mut1_cell31


title: E18.5_mut1_cell29


title: E18.5_mut1_cell28


title: E18.5_mut1_cell27


title: P21-28_ctrl_Sst95


title: P21-28_ctrl_Sst92


title: P21-28_ctrl_Sst93


title: P21-28_ctrl_Sst94


title: E18.5_mut1_cell30


title: P21-28_ctrl_Sst90


title: E18.5_mut1_cell26


title: P21-28_ctrl_Sst89


title: P21-28_ctrl_Sst91


title: E18.5_mut1_cell37


title: E18.5_mut1_cell24


title: E18.5_mut1_cell25


title: E18.5_mut1_cell23


title: P21-28_ctrl_Sst88


title: E18.5_mut1_cell22


title: P21-28_ctrl_Sst84


title: E18.5_mut1_cell20


title: E18.5_mut1_cell18


title: P21-28_ctrl_Sst82


title: P21-28_ctrl_Sst83


title: E18.5_mut1_cell19


title: E18.5_mut1_cell17


title: P21-28_ctrl_Sst81

value: SstCre::tdTomato::Sox6 +/+


title: E18.5_mut1_cell16


title: E18.5_mut1_cell15


title: P21-28_ctrl_Sst80


title: E18.5_mut1_cell14


title: P21-28_ctrl_Sst79


title: P21-28_ctrl_Sst87


title: E18.5_mut1_cell13


title: P21-28_ctrl_Sst76


title: E18.5_mut1_cell12


title: P21-28_ctrl_Sst75


title: P21-28_ctrl_Sst85


title: P21-28_ctrl_Sst78


title: E18.5_mut1_cell21


title: P21-28_ctrl_Sst74


title: P21-28_ctrl_Sst77


title: P21-28_ctrl_Sst86


title: E18.5_mut1_cell11


title: E18.5_mut1_cell10


title: E18.5_mut1_cell9


title: P21-28_ctrl_Sst71


title: P21-28_ctrl_Sst73


title: E18.5_mut1_cell7


title: E18.5_mut1_cell4


title: P21-28_ctrl_Sst70


title: E18.5_mut1_cell8


title: P21-28_ctrl_Sst72


title: E18.5_mut1_cell6


title: P21-28_ctrl_Sst69


title: E18.5_mut1_cell3


title: P21-28_ctrl_Sst68


title: P21-28_ctrl_Sst66


title: P21-28_ctrl_Sst64


title: E18.5_mut1_cell2


title: E18.5_ctrl1_cell128


title: P21-28_ctrl_Sst67


title: P21-28_ctrl_Sst65


title: P21-28_ctrl_Sst63


title: E18.5_mut1_cell1


title: E18.5_ctrl1_cell126


title: E18.5_ctrl1_cell127


title: P21-28_ctrl_Sst59


title: P21-28_ctrl_Sst61


title: P21-28_ctrl_Sst62


title: P21-28_ctrl_Sst60


title: E18.5_ctrl1_cell125


title: E18.5_ctrl1_cell123


title: E18.5_ctrl1_cell124


title: E18.5_mut1_cell5


title: E18.5_ctrl1_cell122


title: P21-28_ctrl_Sst58


title: E18.5_ctrl1_cell121


title: P21-28_ctrl_Sst57


title: P21-28_ctrl_Sst56


title: P21-28_ctrl_Sst53


title: P21-28_ctrl_Sst55


title: P21-28_ctrl_Sst54


title: P21-28_ctrl_Sst52


title: E18.5_ctrl1_cell118


title: E18.5_ctrl1_cell113


title: P21-28_ctrl_Sst48


title: E18.5_ctrl1_cell116


title: P21-28_ctrl_Sst47


title: P21-28_ctrl_Sst49


title: P21-28_ctrl_Sst46


title: E18.5_ctrl1_cell110


title: E18.5_ctrl1_cell111


title: E18.5_ctrl1_cell119


title: E18.5_ctrl1_cell109


title: P21-28_ctrl_Sst51


title: P21-28_ctrl_Sst45


title: P21-28_ctrl_Sst44


title: E18.5_ctrl1_cell120


title: E18.5_ctrl1_cell108


title: P21-28_ctrl_Sst43


title: E18.5_ctrl1_cell117


title: E18.5_ctrl1_cell107


title: E18.5_ctrl1_cell106


title: E18.5_ctrl1_cell114


title: E18.5_ctrl1_cell115


title: P21-28_ctrl_Sst42


title: P21-28_ctrl_Sst40


title: E18.5_ctrl1_cell105


title: E18.5_ctrl1_cell104


title: P21-28_ctrl_Sst50


title: P21-28_ctrl_Sst39


title: E18.5_ctrl1_cell112


title: E18.5_ctrl1_cell103


title: E18.5_ctrl1_cell102


title: E18.5_ctrl1_cell101


title: P21-28_ctrl_Sst37


title: P21-28_ctrl_Sst38


title: E18.5_ctrl1_cell100


title: P21-28_ctrl_Sst35


title: P21-28_ctrl_Sst36


title: E18.5_ctrl1_cell99


title: E18.5_ctrl1_cell98


title: P21-28_ctrl_Sst34


title: P21-28_ctrl_Sst33


title: P21-28_ctrl_Sst41


title: P21-28_ctrl_Sst32


title: E18.5_ctrl1_cell97


title: E18.5_ctrl1_cell96


title: P21-28_ctrl_Sst31


title: E18.5_ctrl1_cell95


title: E18.5_ctrl1_cell94


title: P21-28_ctrl_Sst30


title: P21-28_ctrl_Sst29


title: E18.5_ctrl1_cell93


title: E18.5_ctrl1_cell92


title: E18.5_ctrl1_cell91


title: P21-28_ctrl_Sst27


title: E18.5_ctrl1_cell90


title: P21-28_ctrl_Sst28


title: E18.5_ctrl1_cell89


title: P21-28_ctrl_Sst26


title: P21-28_ctrl_Sst24


title: E18.5_ctrl1_cell88


title: P21-28_ctrl_Sst23


title: E18.5_ctrl1_cell86


title: E18.5_ctrl1_cell87


title: P21-28_ctrl_Sst22


title: E18.5_ctrl1_cell85


title: P21-28_ctrl_Sst21


title: E18.5_ctrl1_cell84


title: P21-28_ctrl_Sst20


title: P21-28_ctrl_Sst17


title: P21-28_ctrl_Sst18


title: E18.5_ctrl1_cell81


title: E18.5_ctrl1_cell82


title: E18.5_ctrl1_cell80


title: P21-28_ctrl_Sst16


title: P21-28_ctrl_Sst15


title: E18.5_ctrl1_cell79


title: P21-28_ctrl_Sst25


title: E18.5_ctrl1_cell78


title: P21-28_ctrl_Sst14


title: P21-28_ctrl_Sst13


title: P21-28_ctrl_Sst10


title: P21-28_ctrl_Sst12


title: P21-28_ctrl_Sst11


title: E18.5_ctrl1_cell76


title: E18.5_ctrl1_cell75


title: P21-28_ctrl_Sst9


title: E18.5_ctrl1_cell74


title: P21-28_ctrl_Sst19


title: E18.5_ctrl1_cell83


title: P21-28_ctrl_Sst8


title: E18.5_ctrl1_cell71


title: P21-28_ctrl_Sst7


title: P21-28_ctrl_Sst5


title: E18.5_ctrl1_cell70


title: E18.5_ctrl1_cell72


title: P21-28_ctrl_Sst4


title: E18.5_ctrl1_cell69


title: P21-28_ctrl_Sst3


title: E18.5_ctrl1_cell67


title: P21-28_ctrl_Sst2


title: E18.5_ctrl1_cell66


title: P21-28_ctrl_Sst1


title: E18.5_ctrl1_cell68


title: E18.5_ctrl1_cell77


title: E18.5_ctrl1_cell65


title: E18.5_ctrl1_cell64


title: BCAA-free-prop, TAC, rep2

city: Newark

first: Maha

last: Abdellatif

state: NJ

address: 185 S. Orange Ave., MSB

department: Cell Biology and Molecular Medicine

institute: Rutgers University

description:
1W-PBF-TAC-2
1W-PBF-TAC-vs-1W-PBF-sham.csv
1W-PBF-TAC-vs-1W-PBC-TAC.csv

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Unique gene hit counts were calculated by using featuremCounts from the Subread package v.1.5.2.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between groups of samples was performed (as seen in the processed files). The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: mm10
Supplementary files format and content: The processed data are provided in csv files. The files include the gene ID, log2 fold change, padj, p value, the normalized reads for each each detectable gene in each of the samples being compared, and gene name. The log2 fold change are for the TAC/sham with either diet, or TAC(BCAA-free)/TAC(BCAA-control), or sham(BCAA-free)/sham(BCAA-contro). The samples in each file are identified by the designated library names.

source_name: heart

extract_protocol:
Trizol extraction of total RNA followed by polA selection)
no library preparation performed

treatment_protocol: Mice were either maintained on a BCAA-control (all essential amino acids, incluing BCAA added in concnetration equivlarnt to those found in standard chow diets) supplemented with 1% propionate diet or a BCAA-free diet, in which BCAA were completely elimnated),  supplemented with 1% propionate diet. This was applied 4 days before the sham or TAC surgeries and continued throughout the survival period (1-wk after surgery).

value: heart

tag: strain

tag: Sex

value: male

value: BCAA-free diet with 1% propionate diet, TAC surgery


title: E18.5_ctrl1_cell62

value: SstCre::RCE::Sox6 flox/+


title: BCAA-free-prop, sham, rep3

description:
1W-PBF-Sham-3
1W-PBF-TAC-vs-1W-PBF-sham.csv
1W-PBF-sham-vs-1W-PBC-sham.csv

value: BCAA-free diet with 1% propionate diet, sham surgery


title: E18.5_ctrl1_cell61


title: BCAA-free-prop, TAC, rep3

description:
1W-PBF-TAC-3
1W-PBF-TAC-vs-1W-PBF-sham.csv
1W-PBF-TAC-vs-1W-PBC-TAC.csv


title: E18.5_ctrl1_cell73


title: BCAA-free-prop, TAC, rep1

description:
1W-PBF-TAC-1
1W-PBF-TAC-vs-1W-PBF-sham.csv
1W-PBF-TAC-vs-1W-PBC-TAC.csv


title: P21-28_ctrl_Sst6


title: BCAA-free-prop, sham, rep2

description:
1W-PBF-Sham-2
1W-PBF-TAC-vs-1W-PBF-sham.csv
1W-PBF-sham-vs-1W-PBC-sham.csv

value: BCAA-free dietwith 1% propionate diet, sham surgery


title: BCAA-free-prop, sham, rep1

description:
1W-PBF-Sham-1
1W-PBF-TAC-vs-1W-PBF-sham.csv
1W-PBF-sham-vs-1W-PBC-sham.csv


title: E18.5_ctrl1_cell60


title: BCAA-control-prop, TAC, rep3

description:
1W-PBC-TAC-3
1W-PBC-TAC-vs-1W-PBC-sham.cvs
1W-PBF-TAC-vs-1W-PBC-TAC.csv

value: BCAA-control diet with 1% propionate diet, TAC surgery


title: E18.5_ctrl1_cell59

description:
SmartSeq2
Munguba_Nikouei_E18.5_counts.txt
Munguba_Nikouei_E18.5_cell_annotation.txt


title: E18.5_ctrl1_cell58


title: E18.5_ctrl1_cell57


title: E18.5_ctrl1_cell56


title: BCAA-control-prop, TAC, rep2

description:
1W-PBC-TAC-2
1W-PBC-TAC-vs-1W-PBC-sham.cvs
1W-PBF-TAC-vs-1W-PBC-TAC.csv


title: E18.5_ctrl1_cell55


title: BCAA-control-prop, sham, rep2

description:
1W-PBC-Sham-2
1W-PBC-TAC-vs-1W-PBC-sham.cvs
1W-PBF-sham-vs-1W-PBC-sham.csv

value: BCAA-control diet with 1% propionate diet, sham surgery


title: BCAA-control-prop, sham, rep3

description:
1W-PBC-Sham-3
1W-PBC-TAC-vs-1W-PBC-sham.cvs
1W-PBF-sham-vs-1W-PBC-sham.csv


title: BCAA-control-prop, TAC, rep1

description:
1W-PBC-TAC-1
1W-PBC-TAC-vs-1W-PBC-sham.cvs
1W-PBF-TAC-vs-1W-PBC-TAC.csv


title: BCAA-control-prop, sham, rep1

description:
1W-PBC-Sham-1
1W-PBC-TAC-vs-1W-PBC-sham.cvs
1W-PBF-sham-vs-1W-PBC-sham.csv

value: BCAA-control with 1% propionate diet, sham surgery


title: E18.5_ctrl1_cell54


title: E18.5_ctrl1_cell53


title: E18.5_ctrl1_cell63


title: E18.5_ctrl1_cell52


title: BCAA-free, TAC, rep3 [BFT3]

description:
BFT-vs-BFC.csv
BFT-vs-BCT.csv

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Unique gene hit counts were calculated by using featuremCounts from the Subread package v.1.5.2.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between groups of samples was performed (as seen in the processed files). The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: mm10
Supplementary files format and content: The processed data are provided as cvs files. The files include the gene ID, log2 fold change, padj, p value, the normalized reads for each each detectable gene in each of the samples being compared, and gene name. The log2 fold change are for the TAC/sham with either diet, or TAC(BCAA-free)/TAC(BCAA-control), or sham(BCAA-free)/sham(BCAA-contro). The samples in each file are identified by the designated library names.

extract_protocol:
Trizol extraction of total RNA followed by polyA selection)
no library preparation performed

treatment_protocol: Mice were either maintained on a BCAA-control (all essential amino acids, incluing BCAA added in concnetration equivlarnt to those found in standard chow diets) or a BCAA-free diet, in which BCAA were completely elimnated). This was applied 4 days before the sham or TAC surgeries and continued throughout the survival period (1-wk after surgery).

value: BCAA-free diet, TAC surgery


title: BCAA-free, TAC, rep2 [BFT2]

description:
BFT-vs-BFC.csv
BFT-vs-BCT.csv


title: E18.5_ctrl1_cell51


title: BCAA-free, sham, rep3 [BFS3]

description:
BFT-vs-BFC.csv
BFS-vs-BCS.csv

value: BCAA-free diet, sham surgery


title: E18.5_ctrl1_cell50


title: E18.5_ctrl1_cell49


title: E18.5_ctrl1_cell48


title: BCAA-free, sham, rep1 [BFS1]

description:
BFT-vs-BFC.csv
BFS-vs-BCS.csv


title: BCAA-free, sham, rep2 [BFS2]

description:
BFT-vs-BFC.csv
BFS-vs-BCS.csv


title: E18.5_ctrl1_cell47


title: BCAA-control, TAC, rep3 [BCT3]

description:
BCT-vs-BCS.csv
BFT-vs-BCT.csv

value: BCAA-control diet, TAC surgery


title: E18.5_ctrl1_cell45

value: Neocortex


title: BCAA-control, TAC, rep2 [BCT2]

description:
BCT-vs-BCS.csv
BFT-vs-BCT.csv


title: E18.5_ctrl1_cell43

value: Somatostatin interneuron


title: E18.5_ctrl1_cell46


title: BCAA-control, TAC, rep1 [BCT1]

description:
BCT-vs-BCS.csv
BFT-vs-BCT.csv


title: E18.5_ctrl1_cell42


title: E18.5_ctrl1_cell44


title: BCAA-control, sham, rep3 [BCS3]

description:
BCT-vs-BCS.csv
BFS-vs-BCS.csv

value: BCAA-control diet, sham surgery


title: E18.5_ctrl1_cell41


title: BCAA-control, sham, rep2 [BCS2]

description:
BCT-vs-BCS.csv
BFS-vs-BCS.csv


title: E18.5_ctrl1_cell39


title: E18.5_ctrl1_cell40


title: BCAA-free, TAC, rep1 [BFT1]

description:
BFT-vs-BFC.csv
BFT-vs-BCT.csv


title: E18.5_ctrl1_cell38


title: E18.5_ctrl1_cell37


title: mRNA-RevIH2i2_2

city: CLERMONT-FERRAND

first: Emilie

last: BRASSET

address: 28 place Henri dunant

institute: CNRS 6293 INSERM U1103 Université Clermont Auvergne

description: 3-6 day old female

data_processing:
trim/remove adapters
remove low quality reads
remove N reads
remove polyX
Assembly: dm6
Supplementary files format and content: bam files from mapping of the respective paired-end reads on ZAM_I and ZAM_LTR (Repbase) using HISAT2 (Galaxy Version 2.1.0+galaxy5)
Supplementary files format and content: BigWig files from mapping of the respective paired-end reads on the Drosophila melanogaster dm6 genome using HISAT2 (Galaxy Version 2.1.0+galaxy5)

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were kept at standard conditon at 25°C

extract_protocol:
Total RNA extraction with TRIzol
DNBSEQ

value: ovaries

value: 3-6 day-old


title: mRNA-RevIH2i2_1

description: 3-6 day old female

value: Flies were kept at standard conditon at 25°C


title: E18.5_ctrl1_cell36


title: 272_Hippocampus_3

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

description:
Akk-3
Akk-3_hippo

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm38.84 whole genome using tophat2.
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: *csv: Comma-separated text files include FPKM (Fragments Per Kilobase Million) values for each Sample.

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purify mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Akkermansia muciniphila Membrane Protein for 6 weeks.

value: Hippocampus

value: 15 months

value: Akkermansia muciniphila Membrane Protein treated for 8 weeks


title: E18.5_ctrl1_cell35

value: SstCre::RCE::Sox6 flox/+


title: 260_Hippocampus_2

description:
Akk-2
Akk-2_hippo


title: E18.5_ctrl1_cell34


title: Prism, C&T K27Ac

city: London

first: Ferdinand

last: Marlétaz

address: Gower Street

department: Genetics, Evolution & Environment

country: United Kingdom

institute: University College London

data_processing:
Cut-and-Tag: Reads were aligned using bowtie2 with the parameters ‘--local --very-sensitive --no-mixed --no-discordant   --phred33 -I 10 -X 700 -3 75’
Library strategy: Cut-and-Tag

organism: Paracentrotus lividus

source_name: Whole embryo

extract_protocol:
Cut-and-Tag: The assay was performed using the CUT&Tag-IT™ Kit (Active Motif) and H3K27ac antibody (Active Motif Ref 39135)).
Cut-and-Tag: Following tagmentation, beads were magnetized, washed, and incubated for 1h at 37°C with proteinase K and SDS to digest the chromatin and release DNA fragments. At the end of the incubation, beads were magnetized and DNA was purified using 625 µl DNA binding buffer. Following purification, libraries were amplified by using 25 µl of DNA sample and 2.5 µl of a uniquely barcoded i5 primer and 2.5 µl of a uniquely barcoded i7 primer in a 50 µl PCR reaction with Q5 high-fidelity DNA polymerase.

value: Whole embryo

value: Prism

value: Whole organism

value: WT

value: Normal embryonic development


title: Gastrula, C&T K27Ac

value: Gastrula


title: E18.5_ctrl1_cell33


title: Late_Blastula, C&T K27Ac

value: Late Blastula


title: E18.5_ctrl1_cell32

value: Neocortex


title: 247_Hippocampus_3

description:
Ctrl_3
Ctrl_3_hippo

value: Normal


title: E18.5_ctrl1_cell31

value: Somatostatin interneuron


title: 236_Hippocampus_1

description:
Akk-1
Akk-1_hippo


title: BCAA-control, sham, rep1 [BCS1]

description:
BCT-vs-BCS.csv
BFS-vs-BCS.csv

value: heart

value: male

value: BCAA-control diet, sham surgery


title: E18.5_ctrl1_cell30


title: 243_Hippocampus_2

description:
Ctrl_2
Ctrl_2_hippo

value: Hippocampus


title: mRNA-RevIH2i2_3

description: 3-6 day old female

value: ovaries

value: 3-6 day-old

value: Flies were kept at standard conditon at 25°C


title: Early_Blastula, C&T K27Ac

value: Whole embryo

value: Early Blastula


title: 242_Hippocampus_1

description:
Ctrl_1
Ctrl_1_hippo

value: 15 months


title: Urinary exosome, ultra-high speed centrifugation [P10]

data_processing:
*library strategy: exosome sRNA-seq
Illumina Bcl2FastQ software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the human reference genome using the bwa aligner.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA
Assembly: hg19
Supplementary files format and content: \06.know_miRNA_expression\*\*.miR.expre.xls
Supplementary files format and content: \11.differential_expression\*\**vs*.diff.xls

source_name: Urinary exosome

extract_protocol:
Urine was mixed with RiboTM Exosome Isolation Reagent and exosome isolation was performed according to the manufacturer’s instructions (Ribobio, China). Exosomal RNA was extracted by HiPure Liquid miRNA Kit/HiPure Serum/Plasma miRNA Kit (Megan, China).
Exosomal RNA were used to prepare small RNA libraries by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB,USA) according to manufacturer’s instructions

value: Urinary exosome

tag: subject status

value: patients with renal calculi


title: Urinary exosome, ultra-high speed centrifugation [P11]


title: Pluteus, ATAC-seq

data_processing:
ATAC-seq: Reads obtained for each library were mapped using Bowtie2 (v2.4.1) with the parameters --very-sensitive and -k 10 (Langmead and Salzberg, 2012) and peak calling for open chromatin region was performed using Generich (v0.6) available at https://github.com/jsh58/Genrich using ATAC model (-j), keeping unpaired alignments (-y), removing PCR duplicates (-r) and excluding reads mapped to mitochondria (-e MT). At this step, we pooled biological and technical replicates together as Generich analyses each replicate separately and then combined them by summarising p-values using Fisher’s method.
ATAC-seq: pybed tools was used to generate a set of unified peaks from the peaks called at each stage, classify peaks according to the activity during development and perform intersection with masked repetitive regions and conserved regions, as well as assigning peaks to genes

source_name: Whole larvae

extract_protocol:
ATAC-seq: ATAC-seq was performed following the Omni-ATAC protocol using Digitonin (Promega) in addition to NP40 and Tween in the cell lysis buffer  (Corces et al., 2017). Sea urchin eggs were fertilised in filtered sea water with 2 mM of Paraminobenzoic acid (Sigma) to prevent hardening of the fertilisation envelope. The fertilization envelope was then removed by repeated filtration on a nylon net (70 µM). Embryos at the appropriate stage were collected and washed in NaCl 0,55M twice then dissociated in Calcium-Magnesium artificial sea water by energetic pipetting. For each time point, different numbers of nuclei were tested, typically 50,000, 150,000 and 250,000. The integrity of the nuclei was checked on a microscope after staining the nuclei with Hoechst.
ATAC-seq: After tagmentation the libraries were purified with a Zymo DNA clean up kit then a QPCR was performed on an aliquot  of the eluted libraries using the Ad1 and Ad2.x primers and the corresponding Ct was determined for each sample (Buenrostro et al. 2013). The libraries were then amplified at Ct+ 2 cycles. The quality of the libraries was checked on a 2% agarose gel to verify the size of the fragments and the nucleosome phasing.

value: Whole larvae

value: Pluteus

value: Whole organism

value: WT

value: Normal embryonic development


title: 272_Blood_3

description:
Akk-3
Akk-3_blood

source_name: Blood

value: Blood

value: Akkermansia muciniphila Membrane Protein treated for 8 weeks


title: E18.5_ctrl1_cell28

value: Neocortex

value: Somatostatin interneuron

value: SstCre::RCE::Sox6 flox/+


title: Urinary exosome, ultra-high speed centrifugation [P8]


title: 16_cells, ATAC-seq


title: HCC1395BL-rep3

type: genomic

city: Silver Spring

first: Wenming

last: Xiao

state: MD

address: 10903 New Hampshire Avenue

department: Office of New Drugs

institute: Center for Drug Evaluation and Research, FDA

description:
Genomic DNA extracted from cell lines was genotyped using Infinium CytoSNP-850K Genotyping BeadChips (Illumina).
CRL-2325 cell line

hyb_protocol: DNA resuspended in RA1 was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Te-Flow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour, and scanned using the iScan System (Illumina).

label: C-Bio and A-DNP

source_name: B lymphoblast

label_protocol: 200ng of genomic DNA was whole-genome amplified in a 24-hour reaction at 37°C using Multi-Sample Amplification Mixes 1 and 2 (MA1 and MA2) and Multi- Sample Master Mix (MSM). After incubation, the amplified DNA was fragmented with Fragmentation Solution (FMS), precipitated with isopropanol and Preciptitation Solution (PM1), and resuspended in Resuspension Solution (RA1).

growth_protocol: HCC1395 cells were cultured in RPMI-1640 + 10% FBS.  HCC1395BL cells were cultured in IMDM + 20% FBS.  All cells were maintained at 37°C with 5% CO2 and subcultured every 2–3 days according to ATCC-recommended procedures.

extract_protocol: Pellets of cultured cells were lysed in a solution of 2% TritonX-100/0.1% SDS/0.1 M NaCl/10 mM Tris/1 mM EDTA and genomic DNA extracted over repeated rounds of treatment with a mixture of glass beads and phenol-chloroform-isoamyl alcohol.  The final aqueous layer was further treated with chloroform-indoleacetic acid followed by RNAse treatment and DNA precipitation using sodium acetate (3 M, pH 5.2) and ice-cold ethanol.

tag: gender

value: Female

value: B lymphoblast

tag: disease state

value: normal tissue


title: 260_Blood_2

description:
Akk-2
Akk-2_blood


title: Urinary exosome, ultra-high speed centrifugation [P9]


title: HCC1395-rep3

description:
Genomic DNA extracted from cell lines was genotyped using Infinium CytoSNP-850K Genotyping BeadChips (Illumina).
CRL-2324 cell line

source_name: Breast carcinoma

value: Breast tumor

value: carcinoma


title: E18.5_ctrl1_cell27


title: 236_Blood_1

description:
Akk-1
Akk-1_blood

value: 15 months


title: HCC1395BL-rep2

data_processing: Genomic DNA extracted from cell lines was genotyped using Infinium CytoSNP-850K Genotyping BeadChips (Illumina).


title: E18.5_ctrl1_cell26


title: HCC1395-rep2


title: 247_Blood_3

description:
Ctrl_3
Ctrl_3_blood

value: Normal


title: Urinary exosome, ultra-high speed centrifugation [P6]

value: Urinary exosome

value: patients with renal calculi


title: E18.5_ctrl1_cell25


title: 243_Blood_2

description:
Ctrl_2
Ctrl_2_blood


title: E18.5_ctrl1_cell24


title: HCC1395BL-rep1


title: E18.5_ctrl1_cell29


title: 242_Blood_1

description:
Ctrl_1
Ctrl_1_blood


title: E18.5_ctrl1_cell23


title: Urinary exosome, ultra-high speed centrifugation [P4]


title: HCC1395-rep1


title: Urinary exosome, ultra-high speed centrifugation [P3]


title: Urinary exosome, ultra-high speed centrifugation [P2]


title: Urinary exosome, ultra-high speed centrifugation [P7]


title: E18.5_ctrl1_cell21


title: H1, NAT10-KD, T3.5, rep2

city: Beijing

first: Yuan

last: Zhou

address: 38 college road

institute: Peking University

data_processing:
First, fastp software (v0.21.1) was used to remove the adaptor and low-quality reads to obtain high-quality clean FASTQ reads.
Clean reads were then aligned to the reference genome (hg38) by using HISAT2 software (v2.2.1), with the genome annotation from Ensembl (http://www.ensembl.org, version 107) as the reference gene model.
The aligned SAM-format reads were sorted, transformed to BAM format, and indexed via samtools (v1.12).
FeatureCounts (v2.0.3) software was used for gene expression quantification.
Absolute transcript concentrations per cell were computed by linear-fitting the RNA spike-in TPM values to attomoles.  RNA half-life measures were calculated as described in Wang et al. (Wang et al., 2014).
Assembly: hg38
Supplementary files format and content: Excel file includes half-life estimations based on attomole-transformed gene expression: All_samples.halflife_information.xlsx
Supplementary files format and content: Excel file includes includes raw read counts for all samples: All_samples.halflife_information.xlsx

source_name: early embryo

growth_protocol: human ESC cell lines H1 (WiCell Research Institute) were cultivated in serum-free,defined Pluripotency Growth Master1 (PGM1) (Cellapy,Cat#CA1007500) and grown on plates coated with growth-factor-reduced Matrigel (CORNING,Cat#354248).

extract_protocol:
Total RNA was extracted from 18 samples using TRIzol Reagent (Invitrogen, cat. NO 15596026). RNA was purified and ERCC spike-in was added. A certain amount of RNA samples is denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
The PCR reaction system and program are configured and set up to amplify the product. The corresponding library quality control protocol will be selected depending upon product requirements. Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).
We used the BGISEQ platform for library construction. High-throughput sequencing was performed on each qualified library and the amount of data for each sample was guaranteed to meet the standard.

treatment_protocol: shRNA targeting sequences against NAT10 were designed, synthesized and subcloned into the GV112 vector. Cells transduced with NAT10 shRNA or negative control shRNA lentivirus with GFP (Genechem, Shanghai, China) were cultured for 48h. GFP+ cells then were enriched and expanded in TeSR-E8 medium with 0.5ug/ml puromycin. Transcription was inhibited by ActinomycinD and samples were collected at predetermined time intervels.

value: early embryo

value: human embryonic stem cell

value: NAT10 knockdown

tag: time


title: H1, NAT10-KD, T3.5, rep1


title: Urinary exosome, ultra-high speed centrifugation [P1]


title: Urinary exosome, ultra-high speed centrifugation [C10]

value: normal subjects