title: EC_RNA_YS_cell437


title: EC_RNA_YS_cell436

status: Public on May 17 2021

type: SRA

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2.
For ChIP part, Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1) (ChIP part) and Hisat2 (version 2.0.4) (RNA part).
ChIP part:  Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard. RNA part: reads were counted by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were aggregate bigwig files.

molecule: total RNA

organism: Mus musculus

source_name: yolk sac (YS)

extract_protocol:
Following CoTECH protocol.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: Organs were digested with 0.06 Collagenase II + 0.08% Trypsin and 0.09% Collagenase II + 0.12% Trypsin  at 37 °C.

tag: cell type

value: endothelial cells

tag: tissue

value: yolk sac (YS)

tag: strain

tag: antibody


title: EC_RNA_YS_cell434


title: EC_RNA_YS_cell430


title: EC_RNA_YS_cell431


title: EC_RNA_YS_cell433


title: EC_RNA_YS_cell429


title: EC_RNA_YS_cell426


title: EC_RNA_YS_cell432


title: EC_RNA_YS_cell427


title: EC_RNA_YS_cell423


title: EC_RNA_YS_cell421


title: EC_RNA_YS_cell422


title: EC_RNA_YS_cell424


title: EC_RNA_YS_cell428


title: EC_RNA_YS_cell425


title: EC_RNA_YS_cell417


title: EC_RNA_YS_cell416


title: EC_RNA_YS_cell418


title: EC_RNA_YS_cell419


title: EC_RNA_YS_cell415


title: EC_RNA_YS_cell438


title: EC_RNA_YS_cell435


title: EC_RNA_YS_cell414


title: EC_RNA_YS_cell413


title: EC_RNA_YS_cell412


title: EC_RNA_YS_cell410


title: EC_RNA_YS_cell411


title: EC_RNA_YS_cell420


title: EC_RNA_YS_cell407


title: EC_RNA_YS_cell408


title: EC_RNA_YS_cell406


title: EC_RNA_YS_cell409


title: EC_RNA_YS_cell403


title: EC_RNA_YS_cell404


title: EC_RNA_YS_cell405


title: EC_RNA_YS_cell402


title: EC_RNA_YS_cell399


title: EC_RNA_YS_cell401


title: EC_RNA_YS_cell400


title: EC_RNA_YS_cell395


title: EC_RNA_YS_cell394


title: EC_RNA_YS_cell393


title: EC_RNA_YS_cell392


title: EC_RNA_YS_cell391


title: EC_RNA_YS_cell390


title: EC_RNA_YS_cell396


title: EC_RNA_YS_cell397


title: EC_RNA_YS_cell388


title: EC_RNA_YS_cell387


title: EC_RNA_YS_cell386


title: EC_RNA_YS_cell389


title: EC_RNA_YS_cell384


title: EC_RNA_YS_cell383


title: EC_RNA_YS_cell382


title: EC_RNA_YS_cell381


title: EC_RNA_YS_cell398


title: EC_RNA_YS_cell378


title: EC_RNA_YS_cell375


title: EC_RNA_YS_cell380


title: EC_RNA_YS_cell376


title: EC_RNA_YS_cell377


title: EC_RNA_YS_cell608


title: EC_RNA_YS_cell379


title: EC_RNA_YS_cell373


title: EC_RNA_YS_cell372


title: EC_RNA_YS_cell370


title: EC_RNA_YS_cell371


title: EC_RNA_YS_cell366


title: EC_RNA_YS_cell368


title: EC_RNA_YS_cell365


title: EC_RNA_YS_cell385


title: EC_RNA_YS_cell367


title: EC_RNA_YS_cell362


title: EC_RNA_YS_cell361


title: EC_RNA_YS_cell363


title: EC_RNA_YS_cell360


title: EC_RNA_YS_cell359


title: EC_RNA_YS_cell374


title: EC_RNA_YS_cell358


title: EC_RNA_YS_cell355


title: EC_RNA_YS_cell352


title: EC_RNA_YS_cell350


title: EC_RNA_YS_cell348


title: EC_RNA_YS_cell349


title: EC_RNA_YS_cell347


title: EC_RNA_YS_cell369


title: EC_RNA_YS_cell356


title: EC_RNA_YS_cell345


title: EC_RNA_YS_cell354


title: EC_RNA_YS_cell344


title: EC_RNA_YS_cell357


title: EC_RNA_YS_cell342


title: EC_RNA_YS_cell343


title: EC_RNA_YS_cell346


title: EC_RNA_YS_cell364


title: EC_RNA_YS_cell341


title: EC_RNA_YS_cell340


title: EC_RNA_YS_cell339


title: EC_RNA_YS_cell338


title: EC_RNA_YS_cell351


title: EC_RNA_YS_cell335


title: EC_RNA_YS_cell337


title: EC_RNA_YS_cell336


title: EC_RNA_YS_cell334


title: EC_RNA_YS_cell353


title: EC_RNA_YS_cell333


title: EC_RNA_YS_cell332


title: EC_RNA_YS_cell331


title: EC_RNA_YS_cell474


title: EC_RNA_YS_cell330


title: EC_RNA_YS_cell328


title: EC_RNA_YS_cell327


title: EC_RNA_YS_cell326


title: EC_RNA_YS_cell325


title: EC_RNA_YS_cell322


title: EC_RNA_YS_cell321


title: EC_RNA_YS_cell324


title: EC_RNA_YS_cell323


title: EC_RNA_YS_cell318


title: EC_RNA_YS_cell316


title: EC_RNA_YS_cell315


title: EC_RNA_YS_cell319


title: EC_RNA_YS_cell312


title: EC_RNA_YS_cell313


title: EC_RNA_YS_cell311


title: EC_RNA_YS_cell317


title: EC_RNA_YS_cell309


title: EC_RNA_YS_cell320


title: EC_RNA_YS_cell308


title: EC_RNA_YS_cell310


title: EC_RNA_YS_cell306


title: EC_RNA_YS_cell305


title: EC_RNA_YS_cell307


title: EC_RNA_YS_cell303


title: EC_RNA_YS_cell304


title: EC_RNA_YS_cell329


title: EC_RNA_YS_cell301


title: EC_RNA_YS_cell299


title: EC_RNA_YS_cell298


title: EC_RNA_YS_cell294


title: EC_RNA_YS_cell295


title: EC_RNA_YS_cell296


title: EC_RNA_YS_cell293


title: EC_RNA_YS_cell292


title: EC_RNA_YS_cell291


title: EC_RNA_YS_cell287


title: EC_RNA_YS_cell286


title: EC_RNA_YS_cell290


title: EC_RNA_YS_cell284


title: EC_RNA_YS_cell283


title: EC_RNA_YS_cell289


title: EC_RNA_YS_cell282


title: EC_RNA_YS_cell281


title: EC_RNA_YS_cell280


title: EC_RNA_YS_cell279


title: EC_RNA_YS_cell278


title: EC_RNA_YS_cell277


title: EC_RNA_YS_cell276


title: EC_RNA_YS_cell302


title: EC_RNA_YS_cell300


title: EC_RNA_YS_cell275


title: EC_RNA_YS_cell274


title: EC_RNA_YS_cell273


title: EC_RNA_YS_cell297


title: EC_RNA_YS_cell272


title: EC_RNA_YS_cell271


title: EC_RNA_YS_cell269


title: EC_RNA_YS_cell285


title: EC_RNA_YS_cell288


title: EC_RNA_YS_cell266


title: EC_RNA_YS_cell270


title: EC_RNA_YS_cell267


title: EC_RNA_YS_cell265


title: EC_RNA_YS_cell314


title: EC_RNA_YS_cell260


title: EC_RNA_YS_cell263


title: EC_RNA_YS_cell259


title: EC_RNA_YS_cell262


title: EC_RNA_YS_cell264


title: EC_RNA_YS_cell258


title: EC_RNA_YS_cell257


title: EC_RNA_YS_cell256


title: EC_RNA_YS_cell252


title: EC_RNA_YS_cell254


title: EC_RNA_YS_cell253


title: EC_RNA_YS_cell251


title: EC_RNA_YS_cell249


title: EC_RNA_YS_cell248


title: EC_RNA_YS_cell246


title: EC_RNA_YS_cell250


title: EC_RNA_YS_cell268


title: EC_RNA_YS_cell247


title: EC_RNA_YS_cell243


title: EC_RNA_YS_cell240


title: EC_RNA_YS_cell242


title: EC_RNA_YS_cell261


title: EC_RNA_YS_cell239


title: EC_RNA_YS_cell241


title: EC_RNA_YS_cell238


title: EC_RNA_YS_cell244


title: EC_RNA_YS_cell236


title: EC_RNA_YS_cell237


title: EC_RNA_YS_cell234


title: EC_RNA_YS_cell255


title: EC_RNA_YS_cell229


title: EC_RNA_YS_cell233


title: EC_RNA_YS_cell228


title: EC_RNA_YS_cell227


title: EC_RNA_YS_cell226


title: EC_RNA_YS_cell232


title: EC_RNA_YS_cell225


title: EC_RNA_YS_cell231


title: EC_RNA_YS_cell221


title: EC_RNA_YS_cell224


title: EC_RNA_YS_cell245


title: EC_RNA_YS_cell220


title: EC_RNA_YS_cell222


title: EC_RNA_YS_cell218


title: EC_RNA_YS_cell223


title: EC_RNA_YS_cell219


title: EC_RNA_YS_cell235


title: EC_RNA_YS_cell216


title: EC_RNA_YS_cell213


title: EC_RNA_YS_cell214


title: EC_RNA_YS_cell215


title: EC_RNA_YS_cell212


title: EC_RNA_YS_cell211


title: EC_RNA_YS_cell210


title: EC_RNA_YS_cell230


title: EC_RNA_YS_cell209


title: EC_RNA_YS_cell208


title: EC_RNA_YS_cell206


title: EC_RNA_YS_cell204


title: EC_RNA_YS_cell205


title: EC_RNA_YS_cell203


title: EC_RNA_YS_cell202


title: EC_RNA_YS_cell201


title: EC_RNA_YS_cell198


title: EC_RNA_YS_cell200


title: EC_RNA_YS_cell199


title: EC_RNA_YS_cell197


title: EC_RNA_YS_cell195


title: EC_RNA_YS_cell194


title: EC_RNA_YS_cell217


title: EC_RNA_YS_cell196


title: EC_RNA_YS_cell191


title: EC_RNA_YS_cell193


title: EC_RNA_YS_cell190


title: EC_RNA_YS_cell192


title: EC_RNA_YS_cell186


title: EC_RNA_YS_cell188


title: EC_RNA_YS_cell185


title: EC_RNA_YS_cell189


title: EC_RNA_YS_cell184


title: EC_RNA_YS_cell183


title: EC_RNA_YS_cell207


title: EC_RNA_YS_cell187


title: EC_RNA_YS_cell180


title: EC_RNA_YS_cell182


title: EC_RNA_YS_cell178


title: EC_RNA_YS_cell176


title: EC_RNA_YS_cell177


title: EC_RNA_YS_cell174


title: EC_RNA_YS_cell173


title: EC_RNA_YS_cell172


title: EC_RNA_YS_cell170


title: EC_RNA_YS_cell169


title: EC_RNA_YS_cell167


title: EC_RNA_YS_cell166


title: EC_RNA_YS_cell168


title: EC_RNA_YS_cell165


title: EC_RNA_YS_cell164


title: EC_RNA_YS_cell163


title: EC_RNA_YS_cell162


title: EC_RNA_YS_cell161


title: EC_RNA_YS_cell160


title: EC_RNA_YS_cell157


title: EC_RNA_YS_cell153


title: EC_RNA_YS_cell154


title: EC_RNA_YS_cell158


title: EC_RNA_YS_cell159


title: EC_RNA_YS_cell179


title: EC_RNA_YS_cell156


title: EC_RNA_YS_cell152


title: EC_RNA_YS_cell155


title: EC_RNA_YS_cell151


title: EC_RNA_YS_cell175


title: EC_RNA_YS_cell149


title: EC_RNA_YS_cell150


title: EC_RNA_YS_cell148


title: EC_RNA_YS_cell171


title: EC_RNA_YS_cell147


title: EC_RNA_YS_cell181


title: EC_RNA_YS_cell145


title: EC_RNA_YS_cell146


title: EC_RNA_YS_cell142


title: EC_RNA_YS_cell141


title: EC_RNA_YS_cell143


title: EC_RNA_YS_cell139


title: EC_RNA_YS_cell138


title: EC_RNA_YS_cell140


title: EC_RNA_YS_cell137


title: EC_RNA_YS_cell136


title: EC_RNA_YS_cell135


title: EC_RNA_YS_cell131


title: EC_RNA_YS_cell134


title: EC_RNA_YS_cell126


title: EC_RNA_YS_cell125


title: EC_RNA_YS_cell130


title: EC_RNA_YS_cell133


title: EC_RNA_YS_cell128


title: EC_RNA_YS_cell123


title: EC_RNA_YS_cell127


title: EC_RNA_YS_cell132


title: EC_RNA_YS_cell129


title: EC_RNA_YS_cell144


title: EC_RNA_YS_cell124


title: EC_RNA_YS_cell119


title: EC_RNA_YS_cell118


title: EC_RNA_YS_cell121


title: EC_RNA_YS_cell117


title: EC_RNA_YS_cell115


title: EC_RNA_YS_cell120


title: EC_RNA_YS_cell116


title: EC_RNA_YS_cell113


title: EC_RNA_YS_cell112


title: EC_RNA_YS_cell111


title: EC_RNA_YS_cell109


title: EC_RNA_YS_cell114


title: EC_RNA_YS_cell108


title: EC_RNA_YS_cell107


title: EC_RNA_YS_cell104


title: EC_RNA_YS_cell103


title: EC_RNA_YS_cell105


title: EC_RNA_YS_cell101


title: EC_RNA_YS_cell100


title: EC_RNA_YS_cell122


title: EC_RNA_YS_cell102


title: EC_RNA_YS_cell99


title: EC_RNA_YS_cell98


title: EC_RNA_YS_cell97


title: EC_RNA_YS_cell96


title: EC_RNA_YS_cell93


title: EC_RNA_YS_cell94


title: EC_RNA_YS_cell91


title: EC_RNA_YS_cell92


title: EC_RNA_YS_cell89


title: EC_RNA_YS_cell88


title: EC_RNA_YS_cell110


title: EC_RNA_YS_cell90


title: EC_RNA_YS_cell87


title: EC_RNA_YS_cell86


title: EC_RNA_YS_cell85


title: EC_RNA_YS_cell84


title: EC_RNA_YS_cell82


title: EC_RNA_YS_cell83


title: EC_RNA_YS_cell106


title: EC_RNA_YS_cell80


title: EC_RNA_YS_cell81


title: EC_RNA_YS_cell79


title: EC_RNA_YS_cell76


title: EC_RNA_YS_cell74


title: EC_RNA_YS_cell69


title: EC_RNA_YS_cell77


title: EC_RNA_YS_cell75


title: EC_RNA_YS_cell72


title: EC_RNA_YS_cell71


title: EC_RNA_YS_cell66


title: EC_RNA_YS_cell78


title: EC_RNA_YS_cell70


title: EC_RNA_YS_cell73


title: EC_RNA_YS_cell95


title: EC_RNA_YS_cell64


title: EC_RNA_YS_cell61


title: EC_RNA_YS_cell62


title: EC_RNA_YS_cell60


title: EC_RNA_YS_cell57


title: EC_RNA_YS_cell59


title: EC_RNA_YS_cell63


title: EC_RNA_YS_cell56


title: EC_RNA_YS_cell55


title: EC_RNA_YS_cell54


title: EC_RNA_YS_cell68


title: EC_RNA_YS_cell53


title: EC_RNA_YS_cell67


title: EC_RNA_YS_cell50


title: EC_RNA_YS_cell48


title: EC_RNA_YS_cell51


title: EC_RNA_YS_cell52


title: EC_RNA_YS_cell45


title: EC_RNA_YS_cell47


title: EC_RNA_YS_cell46


title: EC_RNA_YS_cell65


title: EC_RNA_YS_cell42


title: EC_RNA_YS_cell39


title: EC_RNA_YS_cell41


title: EC_RNA_YS_cell49


title: EC_RNA_YS_cell37


title: EC_RNA_YS_cell34


title: EC_RNA_YS_cell40


title: EC_RNA_YS_cell58


title: EC_RNA_YS_cell38


title: EC_RNA_YS_cell43


title: EC_RNA_YS_cell36


title: EC_RNA_YS_cell33


title: EC_RNA_YS_cell31


title: EC_RNA_YS_cell30


title: EC_RNA_YS_cell44


title: EC_RNA_YS_cell29


title: EC_RNA_YS_cell27


title: EC_RNA_YS_cell28


title: EC_RNA_YS_cell26


title: EC_RNA_YS_cell21


title: EC_RNA_YS_cell25


title: EC_RNA_YS_cell32


title: EC_RNA_YS_cell22


title: EC_RNA_YS_cell23


title: EC_RNA_YS_cell20


title: EC_RNA_YS_cell24


title: EC_RNA_YS_cell35


title: EC_RNA_YS_cell19


title: EC_RNA_YS_cell18


title: EC_RNA_YS_cell15


title: EC_RNA_YS_cell16


title: EC_RNA_YS_cell14


title: EC_RNA_YS_cell17


title: EC_RNA_YS_cell12


title: EC_RNA_YS_cell9


title: EC_RNA_YS_cell8


title: EC_RNA_YS_cell4


title: EC_RNA_YS_cell5


title: EC_RNA_YS_cell13


title: EC_RNA_YS_cell11


title: EC_RNA_YS_cell10


title: EC_RNA_YS_cell7


title: EC_RNA_YS_cell6


title: EC_RNA_YS_cell2


title: EC_RNA_YS_cell3


title: EC_RNA_YS_cell1


title: EC_RNA_AGM_cell512

source_name: aorta-gonad-mesonephros (AGM)

value: aorta-gonad-mesonephros (AGM)


title: EC_RNA_AGM_cell511


title: EC_RNA_AGM_cell510


title: EC_RNA_AGM_cell508


title: EC_RNA_AGM_cell506


title: EC_RNA_AGM_cell507


title: EC_RNA_AGM_cell501


title: EC_RNA_AGM_cell502


title: EC_RNA_AGM_cell505


title: EC_RNA_AGM_cell504


title: EC_RNA_AGM_cell499


title: EC_RNA_AGM_cell498


title: EC_RNA_AGM_cell503


title: EC_RNA_AGM_cell497


title: EC_RNA_AGM_cell496


title: EC_RNA_AGM_cell495


title: EC_RNA_AGM_cell493


title: EC_RNA_AGM_cell500


title: EC_RNA_AGM_cell494


title: EC_RNA_AGM_cell492


title: EC_RNA_AGM_cell491


title: EC_RNA_AGM_cell490


title: EC_RNA_AGM_cell489


title: EC_RNA_AGM_cell488


title: EC_RNA_AGM_cell486


title: EC_RNA_AGM_cell487


title: EC_RNA_AGM_cell509


title: EC_RNA_AGM_cell485


title: EC_RNA_AGM_cell480


title: EC_RNA_AGM_cell483


title: EC_RNA_AGM_cell479


title: EC_RNA_AGM_cell477


title: EC_RNA_AGM_cell482


title: EC_RNA_AGM_cell470


title: EC_RNA_AGM_cell475


title: EC_RNA_AGM_cell472


title: EC_RNA_AGM_cell469


title: EC_RNA_AGM_cell468


title: EC_RNA_AGM_cell467


title: EC_RNA_AGM_cell464


title: EC_RNA_AGM_cell466


title: EC_RNA_AGM_cell471


title: EC_RNA_AGM_cell474


title: EC_RNA_AGM_cell463


title: EC_RNA_AGM_cell460


title: EC_RNA_AGM_cell461


title: EC_RNA_AGM_cell462


title: EC_RNA_AGM_cell484


title: EC_RNA_AGM_cell459


title: EC_RNA_AGM_cell458


title: EC_RNA_AGM_cell481


title: EC_RNA_AGM_cell457


title: EC_RNA_AGM_cell456


title: EC_RNA_AGM_cell455


title: EC_RNA_AGM_cell478


title: EC_RNA_AGM_cell452


title: EC_RNA_AGM_cell454


title: EC_RNA_AGM_cell476


title: EC_RNA_AGM_cell451


title: EC_RNA_AGM_cell453


title: EC_RNA_AGM_cell473


title: EC_RNA_AGM_cell450


title: EC_RNA_AGM_cell465


title: EC_RNA_AGM_cell447


title: EC_RNA_AGM_cell448


title: EC_RNA_AGM_cell445


title: EC_RNA_AGM_cell444


title: EC_RNA_AGM_cell440


title: EC_RNA_AGM_cell439


title: EC_RNA_AGM_cell442


title: EC_RNA_AGM_cell443


title: EC_RNA_AGM_cell437


title: EC_RNA_AGM_cell435


title: EC_RNA_AGM_cell436


title: EC_RNA_AGM_cell433


title: EC_RNA_AGM_cell432


title: EC_RNA_AGM_cell431


title: EC_RNA_AGM_cell430


title: EC_RNA_AGM_cell428


title: EC_RNA_AGM_cell429


title: EC_RNA_AGM_cell441


title: EC_RNA_AGM_cell426


title: EC_RNA_AGM_cell427


title: EC_RNA_AGM_cell425


title: EC_RNA_AGM_cell422


title: EC_RNA_AGM_cell424


title: EC_RNA_AGM_cell449


title: EC_RNA_AGM_cell446


title: EC_RNA_AGM_cell421


title: EC_RNA_AGM_cell420


title: EC_RNA_AGM_cell419


title: EC_RNA_AGM_cell417


title: EC_RNA_AGM_cell418


title: EC_RNA_AGM_cell416


title: EC_RNA_AGM_cell438


title: EC_RNA_AGM_cell414


title: EC_RNA_AGM_cell413


title: EC_RNA_AGM_cell412


title: EC_RNA_AGM_cell410


title: EC_RNA_AGM_cell411


title: EC_RNA_AGM_cell408


title: EC_RNA_AGM_cell407


title: EC_RNA_AGM_cell406


title: EC_RNA_AGM_cell405


title: EC_RNA_AGM_cell423


title: EC_RNA_AGM_cell403


title: EC_RNA_AGM_cell404


title: EC_RNA_AGM_cell400


title: EC_RNA_AGM_cell401


title: EC_RNA_AGM_cell399


title: EC_RNA_AGM_cell398


title: EC_RNA_AGM_cell397


title: EC_RNA_AGM_cell394


title: EC_RNA_AGM_cell402


title: EC_RNA_AGM_cell393


title: EC_RNA_AGM_cell396


title: EC_RNA_AGM_cell415


title: EC_RNA_AGM_cell392


title: EC_RNA_AGM_cell390


title: EC_RNA_AGM_cell391


title: EC_RNA_AGM_cell389


title: EC_RNA_AGM_cell388


title: EC_RNA_AGM_cell395


title: EC_RNA_AGM_cell409


title: EC_RNA_AGM_cell386


title: EC_RNA_AGM_cell385


title: EC_RNA_AGM_cell384


title: EC_RNA_AGM_cell381


title: EC_RNA_AGM_cell380


title: EC_RNA_AGM_cell382


title: EC_RNA_AGM_cell379


title: EC_RNA_AGM_cell378


title: EC_RNA_AGM_cell377


title: EC_RNA_AGM_cell376


title: EC_RNA_AGM_cell373


title: EC_RNA_AGM_cell375


title: EC_RNA_AGM_cell372


title: EC_RNA_AGM_cell370


title: EC_RNA_AGM_cell371


title: EC_RNA_AGM_cell374


title: EC_RNA_AGM_cell367


title: EC_RNA_AGM_cell369


title: EC_RNA_AGM_cell434


title: EC_RNA_AGM_cell387


title: EC_RNA_AGM_cell365


title: EC_RNA_AGM_cell363


title: EC_RNA_AGM_cell368


title: EC_RNA_AGM_cell366


title: EC_RNA_AGM_cell364


title: EC_RNA_AGM_cell359


title: EC_RNA_AGM_cell361


title: EC_RNA_AGM_cell383


title: EC_RNA_AGM_cell360


title: EC_RNA_AGM_cell357


title: EC_RNA_AGM_cell358


title: EC_RNA_AGM_cell356


title: EC_RNA_AGM_cell355


title: EC_RNA_AGM_cell353


title: EC_RNA_AGM_cell352


title: EC_RNA_AGM_cell351


title: EC_RNA_AGM_cell350


title: EC_RNA_AGM_cell348


title: EC_RNA_AGM_cell345


title: EC_RNA_AGM_cell346


title: EC_RNA_AGM_cell344


title: EC_RNA_AGM_cell349


title: EC_RNA_AGM_cell347


title: EC_RNA_AGM_cell343


title: EC_RNA_AGM_cell341


title: EC_RNA_AGM_cell338


title: EC_RNA_AGM_cell342


title: EC_RNA_AGM_cell362


title: EC_RNA_AGM_cell336


title: EC_RNA_AGM_cell337


title: EC_RNA_AGM_cell340


title: EC_RNA_AGM_cell339


title: EC_RNA_AGM_cell331


title: EC_RNA_AGM_cell335


title: EC_RNA_AGM_cell332


title: EC_RNA_AGM_cell334


title: EC_RNA_AGM_cell329


title: EC_RNA_AGM_cell333


title: EC_RNA_AGM_cell330


title: EC_RNA_AGM_cell328


title: EC_RNA_AGM_cell354


title: EC_RNA_AGM_cell322


title: EC_RNA_AGM_cell327


title: EC_RNA_AGM_cell323


title: EC_RNA_AGM_cell324


title: EC_RNA_AGM_cell321


title: EC_RNA_AGM_cell320


title: EC_RNA_AGM_cell326


title: EC_RNA_AGM_cell316


title: EC_RNA_AGM_cell315


title: EC_RNA_AGM_cell325


title: EC_RNA_AGM_cell317


title: EC_RNA_AGM_cell319


title: EC_RNA_AGM_cell312


title: EC_RNA_AGM_cell311


title: EC_RNA_AGM_cell318


title: EC_RNA_AGM_cell309


title: EC_RNA_AGM_cell308


title: EC_RNA_AGM_cell310


title: EC_RNA_AGM_cell307


title: EC_RNA_AGM_cell306


title: EC_RNA_AGM_cell305


title: EC_RNA_AGM_cell304


title: EC_RNA_AGM_cell303


title: EC_RNA_AGM_cell302


title: EC_RNA_AGM_cell301


title: EC_RNA_AGM_cell300


title: EC_RNA_AGM_cell298


title: EC_RNA_AGM_cell295


title: EC_RNA_AGM_cell294


title: EC_RNA_AGM_cell299


title: EC_RNA_AGM_cell296


title: EC_RNA_AGM_cell292


title: EC_RNA_AGM_cell293


title: EC_RNA_AGM_cell297


title: EC_RNA_AGM_cell314


title: EC_RNA_AGM_cell290


title: EC_RNA_AGM_cell291


title: EC_RNA_AGM_cell313


title: EC_RNA_AGM_cell285


title: EC_RNA_AGM_cell286


title: EC_RNA_AGM_cell287


title: EC_RNA_AGM_cell282


title: EC_RNA_AGM_cell283


title: EC_RNA_AGM_cell284


title: EC_RNA_AGM_cell279


title: EC_RNA_AGM_cell278


title: EC_RNA_AGM_cell280


title: EC_RNA_AGM_cell277


title: EC_RNA_AGM_cell275


title: EC_RNA_AGM_cell276


title: EC_RNA_AGM_cell274


title: EC_RNA_AGM_cell272


title: EC_RNA_AGM_cell271


title: EC_RNA_AGM_cell273


title: EC_RNA_AGM_cell270


title: EC_RNA_AGM_cell269


title: EC_RNA_AGM_cell289


title: EC_RNA_AGM_cell288


title: EC_RNA_AGM_cell265


title: EC_RNA_AGM_cell267


title: EC_RNA_AGM_cell264


title: EC_RNA_AGM_cell281


title: EC_RNA_AGM_cell263


title: EC_RNA_AGM_cell261


title: EC_RNA_AGM_cell260


title: EC_RNA_AGM_cell259


title: EC_RNA_AGM_cell257


title: EC_RNA_AGM_cell258


title: EC_RNA_AGM_cell254


title: EC_RNA_AGM_cell255


title: EC_RNA_AGM_cell252


title: EC_RNA_AGM_cell248


title: EC_RNA_AGM_cell249


title: EC_RNA_AGM_cell251


title: EC_RNA_AGM_cell250


title: EC_RNA_AGM_cell253


title: EC_RNA_AGM_cell246


title: EC_RNA_AGM_cell266


title: EC_RNA_AGM_cell268


title: EC_RNA_AGM_cell243


title: EC_RNA_AGM_cell244


title: EC_RNA_AGM_cell245


title: EC_RNA_AGM_cell262


title: EC_RNA_AGM_cell242


title: EC_RNA_AGM_cell241


title: EC_RNA_AGM_cell240


title: EC_RNA_AGM_cell239


title: EC_RNA_AGM_cell256


title: EC_RNA_AGM_cell236


title: EC_RNA_AGM_cell238


title: EC_RNA_AGM_cell235


title: EC_RNA_AGM_cell234


title: EC_RNA_AGM_cell233


title: EC_RNA_AGM_cell230


title: EC_RNA_AGM_cell232


title: EC_RNA_AGM_cell231


title: EC_RNA_AGM_cell247


title: EC_RNA_AGM_cell229


title: EC_RNA_AGM_cell226


title: EC_RNA_AGM_cell224


title: EC_RNA_AGM_cell227


title: EC_RNA_AGM_cell222


title: EC_RNA_AGM_cell223


title: EC_RNA_AGM_cell221


title: EC_RNA_AGM_cell220


title: EC_RNA_AGM_cell237


title: EC_RNA_AGM_cell217


title: EC_RNA_AGM_cell218


title: EC_RNA_AGM_cell219


title: EC_RNA_AGM_cell216


title: EC_RNA_AGM_cell213


title: EC_RNA_AGM_cell214


title: EC_RNA_AGM_cell212


title: EC_RNA_AGM_cell215


title: EC_RNA_AGM_cell207


title: EC_RNA_AGM_cell209


title: EC_RNA_AGM_cell210


title: EC_RNA_AGM_cell206


title: EC_RNA_AGM_cell228


title: EC_RNA_AGM_cell211


title: EC_RNA_AGM_cell205


title: EC_RNA_AGM_cell204


title: EC_RNA_AGM_cell203


title: EC_RNA_AGM_cell201


title: EC_RNA_AGM_cell208


title: EC_RNA_AGM_cell202


title: EC_RNA_AGM_cell200


title: EC_RNA_AGM_cell198


title: EC_RNA_AGM_cell199


title: EC_RNA_AGM_cell225


title: EC_RNA_AGM_cell196


title: EC_RNA_AGM_cell195


title: EC_RNA_AGM_cell197


title: EC_RNA_AGM_cell194


title: EC_RNA_AGM_cell193


title: EC_RNA_AGM_cell192


title: EC_RNA_AGM_cell190


title: EC_RNA_AGM_cell189


title: EC_RNA_AGM_cell191


title: EC_RNA_AGM_cell188


title: EC_RNA_AGM_cell187


title: EC_RNA_AGM_cell184


title: EC_RNA_AGM_cell185


title: EC_RNA_AGM_cell183


title: EC_RNA_AGM_cell182


title: EC_RNA_AGM_cell180


title: EC_RNA_AGM_cell181


title: EC_RNA_AGM_cell179


title: EC_RNA_AGM_cell177


title: EC_RNA_AGM_cell175


title: EC_RNA_AGM_cell172


title: EC_RNA_AGM_cell171


title: EC_RNA_AGM_cell178


title: EC_RNA_AGM_cell174


title: EC_RNA_AGM_cell170


title: EC_RNA_AGM_cell176


title: EC_RNA_AGM_cell169


title: EC_RNA_AGM_cell167


title: EC_RNA_AGM_cell173


title: EC_RNA_AGM_cell166


title: EC_RNA_AGM_cell168


title: EC_RNA_AGM_cell165


title: EC_RNA_AGM_cell163


title: EC_RNA_AGM_cell186


title: EC_RNA_AGM_cell162


title: EC_RNA_AGM_cell161


title: EC_RNA_AGM_cell160


title: EC_RNA_AGM_cell164


title: EC_RNA_AGM_cell159


title: EC_RNA_AGM_cell158


title: EC_RNA_AGM_cell156


title: EC_RNA_AGM_cell157


title: EC_RNA_AGM_cell155


title: EC_RNA_AGM_cell154


title: EC_RNA_AGM_cell153


title: EC_RNA_AGM_cell149


title: EC_RNA_AGM_cell151


title: EC_RNA_AGM_cell150


title: EC_RNA_AGM_cell148


title: EC_RNA_AGM_cell146


title: EC_RNA_AGM_cell144


title: EC_RNA_AGM_cell141


title: EC_RNA_AGM_cell140


title: EC_RNA_AGM_cell138


title: EC_RNA_AGM_cell135


title: EC_RNA_AGM_cell136


title: EC_RNA_AGM_cell137


title: EC_RNA_AGM_cell134


title: EC_RNA_AGM_cell133


title: EC_RNA_AGM_cell131


title: EC_RNA_AGM_cell132


title: EC_RNA_AGM_cell129


title: EC_RNA_AGM_cell128


title: EC_RNA_AGM_cell130


title: EC_RNA_AGM_cell127


title: EC_RNA_AGM_cell126


title: EC_RNA_AGM_cell152


title: EC_RNA_AGM_cell124


title: EC_RNA_AGM_cell125


title: EC_RNA_AGM_cell123


title: EC_RNA_AGM_cell145


title: EC_RNA_AGM_cell122


title: EC_RNA_AGM_cell121


title: EC_RNA_AGM_cell142


title: EC_RNA_AGM_cell120


title: EC_RNA_AGM_cell139


title: EC_RNA_AGM_cell143


title: EC_RNA_AGM_cell147


title: EC_RNA_AGM_cell117


title: EC_RNA_AGM_cell118


title: EC_RNA_AGM_cell115


title: EC_RNA_AGM_cell114


title: EC_RNA_AGM_cell113


title: EC_RNA_AGM_cell112


title: EC_RNA_AGM_cell110


title: EC_RNA_AGM_cell111


title: EC_RNA_AGM_cell109


title: EC_RNA_AGM_cell105


title: EC_RNA_AGM_cell106


title: EC_RNA_AGM_cell108


title: EC_RNA_AGM_cell103


title: EC_RNA_AGM_cell100


title: EC_RNA_AGM_cell101


title: EC_RNA_AGM_cell99


title: EC_RNA_AGM_cell102


title: EC_RNA_AGM_cell98


title: EC_RNA_AGM_cell119


title: EC_RNA_AGM_cell96


title: EC_RNA_AGM_cell97


title: EC_RNA_AGM_cell93


title: EC_RNA_AGM_cell91


title: EC_RNA_AGM_cell94


title: EC_RNA_AGM_cell92


title: EC_RNA_AGM_cell95


title: EC_RNA_AGM_cell89


title: EC_RNA_AGM_cell116


title: EC_RNA_AGM_cell87


title: EC_RNA_AGM_cell88


title: EC_RNA_AGM_cell90


title: EC_RNA_AGM_cell107


title: EC_RNA_AGM_cell85


title: EC_RNA_AGM_cell104


title: EC_RNA_AGM_cell84


title: EC_RNA_AGM_cell83


title: EC_RNA_AGM_cell82


title: EC_RNA_AGM_cell81


title: EC_RNA_AGM_cell80


title: EC_RNA_AGM_cell77


title: EC_RNA_AGM_cell76


title: EC_RNA_AGM_cell74


title: EC_RNA_AGM_cell78


title: EC_RNA_AGM_cell75


title: EC_RNA_AGM_cell72


title: EC_RNA_AGM_cell71


title: EC_RNA_AGM_cell70


title: EC_RNA_AGM_cell73


title: EC_RNA_AGM_cell69


title: EC_RNA_AGM_cell66


title: EC_RNA_AGM_cell67


title: EC_RNA_AGM_cell68


title: EC_RNA_AGM_cell65


title: EC_RNA_AGM_cell64


title: EC_RNA_AGM_cell86


title: EC_RNA_AGM_cell60


title: EC_RNA_AGM_cell62


title: EC_RNA_AGM_cell63


title: EC_RNA_AGM_cell56


title: EC_RNA_AGM_cell79


title: EC_RNA_AGM_cell57


title: EC_RNA_AGM_cell59


title: EC_RNA_AGM_cell58


title: EC_RNA_AGM_cell53


title: EC_RNA_AGM_cell54


title: EC_RNA_AGM_cell52


title: EC_RNA_AGM_cell51


title: EC_RNA_AGM_cell49


title: EC_RNA_AGM_cell50


title: EC_RNA_AGM_cell46


title: EC_RNA_AGM_cell48


title: EC_RNA_AGM_cell47


title: EC_RNA_AGM_cell45


title: EC_RNA_AGM_cell44


title: EC_RNA_AGM_cell41


title: EC_RNA_AGM_cell43


title: EC_RNA_AGM_cell42


title: EC_RNA_AGM_cell39


title: EC_RNA_AGM_cell61


title: EC_RNA_AGM_cell40


title: EC_RNA_AGM_cell38


title: EC_RNA_AGM_cell37


title: EC_RNA_AGM_cell35


title: EC_RNA_AGM_cell33


title: EC_RNA_AGM_cell36


title: EC_RNA_AGM_cell55


title: EC_RNA_AGM_cell32


title: EC_RNA_AGM_cell30


title: EC_RNA_AGM_cell31


title: EC_RNA_AGM_cell29


title: EC_RNA_AGM_cell27


title: EC_RNA_AGM_cell25


title: EC_RNA_AGM_cell26


title: EC_RNA_AGM_cell24


title: EC_RNA_AGM_cell28


title: EC_RNA_AGM_cell22


title: EC_RNA_AGM_cell20


title: EC_RNA_AGM_cell21


title: EC_RNA_AGM_cell18


title: EC_RNA_AGM_cell19


title: EC_RNA_AGM_cell17


title: EC_RNA_AGM_cell15


title: EC_RNA_AGM_cell16


title: EC_RNA_AGM_cell34


title: EC_RNA_AGM_cell9


title: EC_RNA_AGM_cell12


title: EC_RNA_AGM_cell10


title: EC_RNA_AGM_cell14


title: EC_RNA_AGM_cell13


title: EC_RNA_AGM_cell8


title: EC_RNA_AGM_cell11


title: EC_RNA_AGM_cell7


title: EC_RNA_AGM_cell5


title: EC_RNA_AGM_cell6


title: EC_RNA_AGM_cell4


title: EC_RNA_AGM_cell2


title: EC_RNA_AGM_cell1


title: EC_RNA_AGM_cell3


title: EC_RNA_AGM_cell23


title: EC_DNA_YS_cell736

library_source: genomic

molecule: genomic DNA


title: EC_DNA_YS_cell734


title: EC_DNA_YS_cell735


title: EC_DNA_YS_cell732


title: EC_DNA_YS_cell733


title: EC_DNA_YS_cell728


title: EC_DNA_YS_cell729


title: EC_DNA_YS_cell731


title: EC_DNA_YS_cell727


title: EC_DNA_YS_cell725


title: EC_DNA_YS_cell726


title: EC_DNA_YS_cell724


title: EC_DNA_YS_cell722


title: EC_DNA_YS_cell721


title: EC_DNA_YS_cell719


title: EC_DNA_YS_cell715


title: EC_DNA_YS_cell720


title: EC_DNA_YS_cell717


title: EC_DNA_YS_cell716


title: EC_DNA_YS_cell723


title: EC_DNA_YS_cell711


title: EC_DNA_YS_cell714


title: EC_DNA_YS_cell712


title: EC_DNA_YS_cell708


title: EC_DNA_YS_cell710


title: EC_DNA_YS_cell709


title: EC_DNA_YS_cell706


title: EC_DNA_YS_cell730


title: EC_DNA_YS_cell707


title: EC_DNA_YS_cell705


title: EC_DNA_YS_cell713


title: EC_DNA_YS_cell704


title: EC_DNA_YS_cell703


title: EC_DNA_YS_cell702


title: EC_DNA_YS_cell701


title: EC_DNA_YS_cell700


title: EC_DNA_YS_cell699


title: EC_DNA_YS_cell698


title: EC_DNA_YS_cell718


title: EC_DNA_YS_cell695


title: EC_DNA_YS_cell694


title: EC_DNA_YS_cell691


title: EC_DNA_YS_cell693


title: EC_DNA_YS_cell690


title: EC_DNA_YS_cell692


title: EC_DNA_YS_cell688


title: EC_DNA_YS_cell687


title: EC_DNA_YS_cell686


title: EC_DNA_YS_cell685


title: EC_DNA_YS_cell683


title: EC_DNA_YS_cell684


title: EC_DNA_YS_cell681


title: EC_DNA_YS_cell682


title: EC_DNA_YS_cell697


title: EC_DNA_YS_cell696


title: EC_DNA_YS_cell677


title: EC_DNA_YS_cell679


title: EC_DNA_YS_cell676


title: EC_DNA_YS_cell678


title: EC_DNA_YS_cell670


title: EC_DNA_YS_cell673


title: EC_DNA_YS_cell675


title: EC_DNA_YS_cell671


title: EC_DNA_YS_cell668


title: EC_DNA_YS_cell674


title: EC_DNA_YS_cell689


title: EC_DNA_YS_cell666


title: EC_DNA_YS_cell665


title: EC_DNA_YS_cell662


title: EC_DNA_YS_cell663


title: EC_DNA_YS_cell664


title: EC_DNA_YS_cell667


title: EC_DNA_YS_cell661


title: EC_DNA_YS_cell660


title: EC_DNA_YS_cell659


title: EC_DNA_YS_cell658


title: EC_DNA_YS_cell680


title: EC_DNA_YS_cell672


title: EC_DNA_YS_cell656


title: EC_DNA_YS_cell654


title: EC_DNA_YS_cell655


title: EC_DNA_YS_cell653


title: EC_DNA_YS_cell669


title: EC_DNA_YS_cell652


title: EC_DNA_YS_cell651


title: EC_DNA_YS_cell644


title: EC_DNA_YS_cell648


title: EC_DNA_YS_cell646


title: EC_DNA_YS_cell643


title: EC_DNA_YS_cell647


title: EC_DNA_YS_cell650


title: EC_DNA_YS_cell641


title: EC_DNA_YS_cell645


title: EC_DNA_YS_cell639


title: EC_DNA_YS_cell635


title: EC_DNA_YS_cell634


title: EC_DNA_YS_cell657


title: EC_DNA_YS_cell632


title: EC_DNA_YS_cell633


title: EC_DNA_YS_cell631


title: EC_DNA_YS_cell638


title: EC_DNA_YS_cell637


title: EC_DNA_YS_cell630


title: EC_DNA_YS_cell629


title: EC_DNA_YS_cell628


title: EC_DNA_YS_cell640


title: EC_DNA_YS_cell649


title: EC_DNA_YS_cell642


title: EC_DNA_YS_cell624


title: EC_DNA_YS_cell623


title: EC_DNA_YS_cell625


title: EC_DNA_YS_cell627


title: EC_DNA_YS_cell622


title: EC_DNA_YS_cell621


title: EC_DNA_YS_cell620


title: EC_DNA_YS_cell636


title: EC_DNA_YS_cell618


title: EC_DNA_YS_cell616


title: EC_DNA_YS_cell615


title: EC_DNA_YS_cell614


title: EC_DNA_YS_cell617


title: EC_DNA_YS_cell613


title: EC_DNA_YS_cell626


title: EC_DNA_YS_cell612


title: EC_DNA_YS_cell609


title: EC_DNA_YS_cell610


title: EC_DNA_YS_cell611


title: EC_DNA_YS_cell607


title: EC_DNA_YS_cell608


title: EC_DNA_YS_cell605


title: EC_DNA_YS_cell604


title: EC_DNA_YS_cell606


title: EC_DNA_YS_cell603


title: EC_DNA_YS_cell601


title: EC_DNA_YS_cell602


title: EC_DNA_YS_cell600


title: EC_DNA_YS_cell598


title: EC_DNA_YS_cell619


title: EC_DNA_YS_cell599


title: EC_DNA_YS_cell595


title: EC_DNA_YS_cell597


title: EC_DNA_YS_cell596


title: EC_DNA_YS_cell593


title: EC_DNA_YS_cell587


title: EC_DNA_YS_cell589


title: EC_DNA_YS_cell588


title: EC_DNA_YS_cell590


title: EC_DNA_YS_cell586


title: EC_DNA_YS_cell591


title: EC_DNA_YS_cell592


title: EC_DNA_YS_cell582


title: EC_DNA_YS_cell585


title: EC_DNA_YS_cell583


title: EC_DNA_YS_cell579


title: EC_DNA_YS_cell577


title: EC_DNA_YS_cell575


title: EC_DNA_YS_cell581


title: EC_DNA_YS_cell584


title: EC_DNA_YS_cell573


title: EC_DNA_YS_cell578


title: EC_DNA_YS_cell574


title: EC_DNA_YS_cell576


title: EC_DNA_YS_cell594


title: EC_DNA_YS_cell572


title: EC_DNA_YS_cell580


title: EC_DNA_YS_cell571


title: EC_DNA_YS_cell569


title: EC_DNA_YS_cell570


title: EC_DNA_YS_cell566


title: EC_DNA_YS_cell567


title: EC_DNA_YS_cell565


title: EC_DNA_YS_cell568


title: EC_DNA_YS_cell559


title: EC_DNA_YS_cell561


title: EC_DNA_YS_cell562


title: EC_DNA_YS_cell560


title: EC_DNA_YS_cell563


title: EC_DNA_YS_cell557


title: EC_DNA_YS_cell558


title: EC_DNA_YS_cell555


title: EC_DNA_YS_cell556


title: EC_DNA_YS_cell553


title: EC_DNA_YS_cell550


title: EC_DNA_YS_cell545


title: EC_DNA_YS_cell547


title: EC_DNA_YS_cell549


title: EC_DNA_YS_cell546


title: EC_DNA_YS_cell548


title: EC_DNA_YS_cell544


title: EC_DNA_YS_cell564


title: EC_DNA_YS_cell543


title: EC_DNA_YS_cell540


title: EC_DNA_YS_cell538


title: EC_DNA_YS_cell537


title: EC_DNA_YS_cell541


title: EC_DNA_YS_cell539


title: EC_DNA_YS_cell536


title: EC_DNA_YS_cell535


title: EC_DNA_YS_cell531


title: EC_DNA_YS_cell533


title: EC_DNA_YS_cell532


title: EC_DNA_YS_cell530


title: EC_DNA_YS_cell529


title: EC_DNA_YS_cell552


title: EC_DNA_YS_cell554


title: EC_DNA_YS_cell526


title: EC_DNA_YS_cell525


title: EC_DNA_YS_cell551


title: EC_DNA_YS_cell524


title: EC_DNA_YS_cell542


title: EC_DNA_YS_cell528


title: EC_DNA_YS_cell527


title: EC_DNA_YS_cell518


title: EC_DNA_YS_cell519


title: EC_DNA_YS_cell523


title: EC_DNA_YS_cell517


title: EC_DNA_YS_cell534


title: EC_DNA_YS_cell514


title: EC_DNA_YS_cell515


title: EC_DNA_YS_cell521


title: EC_DNA_YS_cell520


title: EC_DNA_YS_cell511


title: EC_DNA_YS_cell510


title: EC_DNA_YS_cell513


title: EC_DNA_YS_cell512


title: EC_DNA_YS_cell509


title: EC_DNA_YS_cell507


title: EC_DNA_YS_cell504


title: EC_DNA_YS_cell502


title: EC_DNA_YS_cell503


title: EC_DNA_YS_cell508


title: EC_DNA_YS_cell506


title: EC_DNA_YS_cell501


title: EC_DNA_YS_cell499


title: EC_DNA_YS_cell498


title: EC_DNA_YS_cell516


title: EC_DNA_YS_cell522


title: EC_DNA_YS_cell497


title: EC_DNA_YS_cell496


title: EC_DNA_YS_cell495


title: EC_DNA_YS_cell494


title: EC_DNA_YS_cell492


title: EC_DNA_YS_cell493


title: EC_DNA_YS_cell491


title: EC_DNA_YS_cell490


title: EC_DNA_YS_cell505


title: EC_DNA_YS_cell488


title: EC_DNA_YS_cell489


title: EC_DNA_YS_cell486


title: EC_DNA_YS_cell482


title: EC_DNA_YS_cell485


title: EC_DNA_YS_cell481


title: EC_DNA_YS_cell480


title: EC_DNA_YS_cell484


title: EC_DNA_YS_cell477


title: EC_DNA_YS_cell476


title: EC_DNA_YS_cell478


title: EC_DNA_YS_cell475


title: EC_DNA_YS_cell500


title: EC_DNA_YS_cell479


title: EC_DNA_YS_cell472


title: EC_DNA_YS_cell473


title: EC_DNA_YS_cell470


title: EC_DNA_YS_cell471


title: EC_DNA_YS_cell469


title: EC_DNA_YS_cell468


title: EC_DNA_YS_cell466


title: EC_DNA_YS_cell487


title: EC_DNA_YS_cell465


title: EC_DNA_YS_cell464


title: EC_DNA_YS_cell483


title: EC_DNA_YS_cell463


title: EC_DNA_YS_cell462


title: EC_DNA_YS_cell461


title: EC_DNA_YS_cell460


title: EC_DNA_YS_cell457


title: EC_DNA_YS_cell458


title: EC_DNA_YS_cell456


title: EC_DNA_YS_cell474


title: EC_DNA_YS_cell455


title: EC_DNA_YS_cell453


title: EC_DNA_YS_cell459


title: EC_DNA_YS_cell451


title: EC_DNA_YS_cell454


title: EC_DNA_YS_cell452


title: EC_DNA_YS_cell448


title: EC_DNA_YS_cell449


title: EC_DNA_YS_cell446


title: EC_DNA_YS_cell445


title: EC_DNA_YS_cell447


title: EC_DNA_YS_cell450


title: EC_DNA_YS_cell443


title: EC_DNA_YS_cell441


title: EC_DNA_YS_cell442


title: EC_DNA_YS_cell444


title: EC_DNA_YS_cell467


title: EC_DNA_YS_cell440


title: EC_DNA_YS_cell438


title: EC_DNA_YS_cell439


title: EC_DNA_YS_cell436


title: EC_DNA_YS_cell435


title: EC_DNA_YS_cell432


title: EC_DNA_YS_cell434


title: EC_DNA_YS_cell433


title: EC_DNA_YS_cell431


title: EC_DNA_YS_cell430


title: EC_DNA_YS_cell429


title: EC_DNA_YS_cell427


title: EC_DNA_YS_cell426


title: EC_DNA_YS_cell428


title: EC_DNA_YS_cell423


title: EC_DNA_YS_cell424


title: EC_DNA_YS_cell422


title: EC_DNA_YS_cell420


title: EC_DNA_YS_cell425


title: EC_DNA_YS_cell416


title: EC_DNA_YS_cell421


title: EC_DNA_YS_cell419


title: EC_DNA_YS_cell415


title: EC_DNA_YS_cell414


title: EC_DNA_YS_cell413


title: EC_DNA_YS_cell437


title: EC_DNA_YS_cell418


title: EC_DNA_YS_cell411


title: EC_DNA_YS_cell410


title: EC_DNA_YS_cell412


title: EC_DNA_YS_cell407


title: EC_DNA_YS_cell406


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title: EC_DNA_YS_cell2


title: EC_DNA_YS_cell21


title: EC_DNA_YS_cell3


title: EC_DNA_YS_cell4


title: EC_DNA_YS_cell7


title: EC_DNA_AGM_cell510


title: EC_DNA_AGM_cell508


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title: EC_DNA_YS_cell13


title: EC_DNA_AGM_cell504


title: EC_DNA_AGM_cell502


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title: EC_DNA_YS_cell9


title: EC_DNA_AGM_cell494


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title: EC_DNA_AGM_cell503


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title: EC_DNA_AGM_cell492


title: EC_DNA_AGM_cell491


title: EC_DNA_YS_cell1


title: EC_DNA_AGM_cell509


title: EC_DNA_AGM_cell490


title: EC_DNA_AGM_cell487


title: EC_DNA_AGM_cell485


title: EC_DNA_AGM_cell489


title: EC_DNA_AGM_cell486


title: EC_DNA_AGM_cell507


title: EC_DNA_AGM_cell484


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title: EC_DNA_AGM_cell483


title: EC_DNA_AGM_cell480


title: EC_DNA_AGM_cell479


title: EC_DNA_AGM_cell478


title: EC_DNA_AGM_cell482


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title: EC_DNA_AGM_cell469


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title: EC_DNA_AGM_cell473


title: EC_DNA_AGM_cell468


title: EC_DNA_AGM_cell467


title: EC_DNA_AGM_cell464


title: EC_DNA_AGM_cell461


title: EC_DNA_AGM_cell462


title: EC_DNA_AGM_cell460


title: EC_DNA_AGM_cell463


title: EC_DNA_AGM_cell457


title: EC_DNA_AGM_cell459


title: EC_DNA_AGM_cell466


title: EC_DNA_AGM_cell465


title: EC_DNA_AGM_cell458


title: EC_DNA_AGM_cell456


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title: EC_DNA_AGM_cell426


title: EC_DNA_AGM_cell434


title: EC_DNA_AGM_cell433


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title: EC_DNA_AGM_cell410


title: EC_DNA_AGM_cell409


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title: EC_DNA_AGM_cell405


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title: EC_DNA_AGM_cell418


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title: EC_DNA_AGM_cell375


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title: EC_DNA_AGM_cell372


title: EC_DNA_AGM_cell393


title: EC_DNA_AGM_cell374


title: EC_DNA_AGM_cell370


title: EC_DNA_AGM_cell391


title: EC_DNA_AGM_cell369


title: EC_DNA_AGM_cell367


title: EC_DNA_AGM_cell371


title: EC_DNA_AGM_cell368


title: Xyloglucan-oligosaccharides_rep_D1

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

data_processing:
Paired-end reads (2x100pb) were filtered by quality and presence of adaptors using Trimmomatic v0.38 and rRNA reads were filtered using SortmeRNA v. 2.0.
QC reads were mapped into the Xanthomonas citri pv. citri str. 306 genome using Bowtie2 algorithm.
Differential gene expression analysis was based on counting data and performed using the Bioconductor DESeq2 package using the R platform, by paired comparison against the control (Glucose) condition.
Transcripts showing differential expression (log2-fold change ≥1 and ≤-1) relative to the control condition (Glucose) were determined by applying p-ajusted ≤ 0.05 as the threshold.
Genome_build: Xanthomonas
Genome_build: European Nucleotide Archive ASM716v1
Genome_build: genome-build-accession GCA_000007165.1
Supplementary_files_format_and_content: Matrix tab-delimited file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix tab-delimited file include TPM values for each Sample
Supplementary_files_format_and_content: Matrix tab-delimited file include DESeq2 results

organism: Xanthomonas citri pv. citri

source_name: Bacterial culture

growth_protocol: X. citri was cultivated in LB-medium without sodium chloride (LB ON) with 100 µg/mL of ampicillin, being maintained at 30 °C and 200 rpm for 16 hours. The bacterial cultures were centrifuged and washed with XVM2m medium once, and then inoculated in the XVM2m medium containing glucose or xylooligosaccharides as sole carbohydrate source with an initial optical density at 600 nm of 0.01. Bacteria were grown with constant shaking at 200 rpm and 30 °C and were harvested when reached the mid-exponential phase.

extract_protocol:
RNA was harvested from X. citri cultures at mid-exponential phase using the Trizol/chloroform protocol.  Genomic DNA was then removed, followed by purification of the samples with the RNeasy Mini Kit (Qiagen). Then, 2-2.5 µg of RNA was used for depletion of rRNA using the Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria - Epicenter Biotechnologies).
The preparation of the cDNA libraries was achieved with the Illumina TruSeq Stranded Total RNA kit according to the manufacturer's protocol.  Libraries were sequenced on the Illumina HiSeq 2500.

tag: carbon source

value: Xyloglucan-oligosaccharides

tag: biological replicate


title: EC_DNA_AGM_cell365


title: EC_DNA_AGM_cell364


title: EC_DNA_AGM_cell363


title: Xyloglucan-oligosaccharides_rep_C1


title: EC_DNA_AGM_cell383


title: EC_DNA_AGM_cell379


title: EC_DNA_AGM_cell362


title: EC_DNA_AGM_cell377


title: EC_DNA_AGM_cell358


title: EC_DNA_AGM_cell357


title: EC_DNA_AGM_cell361


title: EC_DNA_AGM_cell356


title: Xyloglucan-oligosaccharides_rep_B0


title: EC_DNA_AGM_cell359


title: EC_DNA_AGM_cell360


title: EC_DNA_AGM_cell355


title: Young ASC3_lncRNA

city: wuhan

first: sen

last: ren

state: hubei

address: donghu road

department: Department of Neurosurgery

institute: Zhongnan Hospital of Wuhan University

description:
Sample 9-Y_ASC3
mRNA, lncRNA, circRNA

data_processing:
Illumina Xten software used for basecalling.
Transcriptome sequencing uses high-throughput sequencing technology to sequence the cDNA after total RNA reverse transcription, and obtains most transcripts of samples in this state.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome, TPM and FPKM were calculated using Bowtie2 (Langmead B et al., 2012)
Genome_build: hg19
Supplementary_files_format_and_content: text files include counts,  FPKM and TPM values

organism: Homo sapiens

source_name: adipose stem cells

extract_protocol:
Adipose stem cell samples were randomly selected from old group (n = 3), young group (n = 3) and diabetic group (n = 3), rinsed with PBS twice and total RNA was isolated by using miRNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Subcutaneous adipose tissue

tag: disease state

value: Normal

tag: age/years old


title: Young ASC2_lncRNA

description:
Sample 8-Y_ASC2
mRNA, lncRNA, circRNA


title: Xyloglucan-oligosaccharides_rep_B1


title: Young ASC1_lncRNA

description:
Sample 7-Y_ASC1
mRNA, lncRNA, circRNA


title: EC_DNA_AGM_cell366


title: Old ASC2_lncRNA

description:
Sample 5-O_ASC2
mRNA, lncRNA, circRNA


title: Old ASC3_lncRNA

description:
Sample 6-O_ASC3
mRNA, lncRNA, circRNA


title: EC_DNA_AGM_cell352


title: EC_DNA_AGM_cell354


title: EC_DNA_AGM_cell350


title: EC_DNA_AGM_cell351


title: EC_DNA_AGM_cell353


title: EC_DNA_AGM_cell349


title: Diabetic ASC3_lncRNA

description:
Sample 3-D_ASC3
mRNA, lncRNA, circRNA

value: Diabetes mellitus


title: Diabetic ASC2_lncRNA

description:
Sample 2-D_ASC2
mRNA, lncRNA, circRNA


title: EC_DNA_AGM_cell347


title: Diabetic ASC1_lncRNA

description:
Sample 1-D_ASC1
mRNA, lncRNA, circRNA


title: EC_DNA_AGM_cell346


title: EC_DNA_AGM_cell345


title: EC_DNA_AGM_cell342


title: EC_DNA_AGM_cell343


title: EC_DNA_AGM_cell344


title: D1_MTZ_Plus_rep2_11_7_19_S12_R1_001

city: Pittsburgh

first: Jeffrey

last: Gross

state: PA

department: Ophthalmology

country: USA

institute: University of Pittsburgh School Of Medicine

data_processing:
All processing of raw data was performed using the CLC Genomics Workbench (v20) Toolbox
Reads were trimmed using quality trim limit = 0.05, ambiguous trim = 2, and automatic read-through adapter trimming enabled (Trim Reads tool v2.4)
Reads were mapped to the zebrafish reference genome, GRCz11, and TPM expression values were caluclated using the RNA-seq Analysis tool (v2.2) in CLC Genomics Workbench
Genome_build: GRCz11
Supplementary_files_format_and_content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint

organism: Danio rerio

source_name: macrophage microglia cell

growth_protocol: Embryos/larvae were treated with 1.5X phenylthiourea (PTU) in system water from 0.25-5dpf to stop pigmentation. After 5dpf, larvae were maintained in system water for the remaining duration of the experiment.

extract_protocol:
≤1000 mCherry-positive cells from dissociated enuculeated larval eyes were FACS-sorted directly into buffer from the SMART-Seq HT Ultra Low Input RNA Kit from Takara Bio, Inc. cDNA synthesis, amplification, and purification was performed using the SMART-Seq HT Ultra Low Input RNA Kit.
Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina, following manufacterer's instructions

treatment_protocol: A subset of larvae (3 replicates from each timepoint) were treated with 10mM metronidazole (MTZ) from 5-6dpf (24 hours) to ablate the retinal pigment epithelium

tag: treatment

value: MTZ+

tag: time point

tag: replicate


title: C1_MTZ_Minus_rep2_11_7_19_S11_R1_001

value: MTZ-


title: F1_MTZ_Plus_rep3_11_7_19_S2_R1_001


title: E1_MTZ_Minus_rep3_11_7_19_S1_R1_001


title: Old ASC1_lncRNA

description:
Sample 4-O_ASC1
mRNA, lncRNA, circRNA


title: B1_MTZ_Plus_rep1_11_7_19_S10_R1_001


title: EC_DNA_AGM_cell339


title: B1_Plus_rep3_11_25_19_S6_R1_001


title: A1_MTZ_Minus_rep1_11_7_19_S9_R1_001


title: A1_MTZ_Minus_rep3_11_25_19_S5_R1_001


title: C1_7dpfMTZ_Minus_rep2_11_14_19_S3_R1_001


title: EC_DNA_AGM_cell338


title: D1_7dpfMTZ_Plus_rep2_11_14_19_S4_R1_001


title: EC_DNA_AGM_cell340


title: EC_DNA_AGM_cell336


title: B1_Gross_12_19_19_S8_R1_001


title: EC_DNA_AGM_cell335


title: EC_DNA_AGM_cell348


title: EC_DNA_AGM_cell334


title: Gross_B1_3_1_18_S6_R1_001

data_processing:
All processing of raw data was performed using the CLC Genomics Workbench (v10) Toolbox
Reads were trimmed using quality trim limit = 0.05, ambiguous trim = 2, and automatic read-through adapter trimming enabled (Trim Reads tool v2.1)
Reads were mapped to the zebrafish reference genome, GRCz10, and TPM expression values were caluclated using the RNA-seq Analysis tool (v2.16) in CLC Genomics Workbench
Genome_build: GRCz10
Supplementary_files_format_and_content: tab delimited text files containing TPM and total counts for all genes for all samples from each timepoint

source_name: retinal pigment epithelium

extract_protocol:
≤1000 eGFP-positive cells from dissociated enuculeated larval eyes were FACS-sorted directly into buffer from the SMART-Seq v4 Ultra Low Input RNA Kit from Takara Bio, Inc. cDNA synthesis, amplification, and purification was performed using the SMART-Seq v4 Ultra Low Input RNA Kit.
Libraries were prepared using the Nextera XT DNA Library Preparation Kit from Illumina, following manufacterer's instructions


title: A1_Gross_12_19_19_S7_R1_001


title: EC_DNA_AGM_cell333


title: EC_DNA_AGM_cell332


title: Gross_A1_3_1_18_S5_R1_001


title: Gross_4_2_19_18_S8_R1_001


title: EC_DNA_AGM_cell341


title: Gross_3_2_19_18_S7_R1_001


title: B1_7dpi__Mtz_positive_S4_R1_001


title: EC_DNA_AGM_cell330


title: EC_DNA_AGM_cell337


title: A1_7dpi_Mtz_negative_S3_R1_001


title: Gross_2_2_19_18_S9_R1_001


title: EC_DNA_AGM_cell329


title: EC_DNA_AGM_cell325


title: EC_DNA_AGM_cell328


title: EC_DNA_AGM_cell324


title: 4dpi_Mtz_wellB1_S1_R1_001


title: 4dpi_Mtz_positive_S2_R1_001

description:
title indicates MTZ positive, but naming was in error when sequencing, this is in fact an MTZ- sample
RPE_4dpi_TPM_totalCOUNTS.txt


title: Gross_A1_2_26_18_S2_R1_001


title: Gross_B1_2_26_18_S3_R1_001


title: EC_DNA_AGM_cell326


title: EC_DNA_AGM_cell322


title: EC_DNA_AGM_cell323


title: Gross_4_2_14_18_S3_R1_001


title: Gross_1_2_19_18_S9_R1_001


title: EC_DNA_AGM_cell321


title: EC_DNA_AGM_cell327


title: Gross_3_2_14_18_S1_R1_001


title: EC_DNA_AGM_cell320


title: EC_DNA_AGM_cell319


title: Gross_2_2_14_18_S2_R1_001


title: Gross_1_2_14_18_S1_R1_001


title: EC_DNA_AGM_cell318


title: EC_DNA_AGM_cell331


title: EC_DNA_AGM_cell317


title: C1_2dpi_Mtz_positive_S2_R1_001


title: EC_DNA_AGM_cell316


title: EC_DNA_AGM_cell315


title: EC_DNA_AGM_cell313


title: B1_2dpi_Mtz_negative_S1_R1_001


title: EC_DNA_AGM_cell312


title: EC_DNA_AGM_cell310


title: EC_DNA_AGM_cell308


title: EC_DNA_AGM_cell309


title: EC_DNA_AGM_cell314


title: EC_DNA_AGM_cell305


title: EC_DNA_AGM_cell306


title: EC_DNA_AGM_cell307


title: EC_DNA_AGM_cell304


title: RS3_Input_ Rep3

first: Leilei

last: Zhou

address: No. 20 Nanxincun, Xiangshan, Haidian District

department: Institute of botany

institute: Chinese Academy of Sciences

description: grown in a standard greenhouse

data_processing:
For data analysis, the quality of raw sequencing reads was initially assessed by FastQC tool (version 0.11.7; http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Adaptors and low-quality bases with a score < 20 were trimmed using Cutadapt (version 1.16), and then short reads with a length < 18 nucleotides or reads containing ambiguous nucleotides were filtered out by Trimmomatic (version 0.30)
The remaining reads were aligned to the strawberry reference genome v1.1 (ftp://ftp.bioinfo.wsu.edu/species/Fragaria_vesca/Fvesca-genome.v1.1) by Burrows Wheeler Aligner (BWA; version 0.30). Mapping quality (MAPQ) of all aligned reads was concurrently evaluated, and only uniquely mapped reads with a MAPQ ≥ 13 were retained for subsequent analysis.
The identification of m6A peaks was carried out by MACS software (version 2.0.10), using the corresponding input as a control. High-confidence peaks were obtained by a stringent cutoff threshold for MACS-assigned false discovery rate (FDR) < 0.05.
PeakAnalyzer (version 2.0) was applied to annotate the identified peaks to the strawberry genome annotation file (ftp.bioinfo.wsu.edu/species/Fragaria_vesca/Fvesca-genome.v2.0.a2/genes/).
Genome_build: Fvesca-genome v1.1
Supplementary_files_format_and_content: Tab-delimited tsv files include called peaks for each Sample

organism: Fragaria vesca

source_name: Total RNA from RS3 fruit

extract_protocol:
Total RNA was extracted with the plant RNA extraction kit (Magen, R4165-02) from woodland strawberry fruit at S6, RS1, and RS3 stages, respectively. mRNA was isolated from the total RNA and then fragmented, followed by immunoprecipitation with specific anti-m6A antibody (Synaptic Systems, 202003).
For library construction, 50 ng of immunoprecipitated mRNAs or pre-immunoprecipitated mRNAs (input control) were used for library construction with NEBNext ultra RNA library prepare kit for illumina (NEB, E7530). High-throughput sequencing was performed on the illumina HiSeq X sequencer with a paired-end read length of 150 bp according to the standard protocols.

value: Fruits with the removal of attached achenes

tag: developmental stage

value: 27 DPA


title: RS3_Input_ Rep2

description: grown in a standard greenhouse


title: EC_DNA_AGM_cell303


title: EC_DNA_AGM_cell302


title: Young_P1

type: RNA

city: Kyoto

first: Kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

country: Japan

institute: Graduate School of Medicine, Kyoto University

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1 . Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.

source_name: CD8 subset cells from spleen & lymph node

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: Total RNAs were isolated from cells using Nucleospin RNA (Macherey-Nagel) and used for cDNA synthesis using RevatraAce reverse transcriptase (Toyobo) and random primer according to the manufacture’s instructions.

treatment_protocol: No treatment

tag: strain background

tag: genotype/variation

tag: age

value: 1 to 3 months old

value: Spleen & lymph node

tag: cd8 t-cell subset

value: CD44low CD62Lhigh


title: Aged_WT with tumor

source_name: CD8 T-cells from draining lymph node

value: WT

value: 17 months old

tag: tumor cell injection

value: MC38 cell injection

value: Lymph node


title: Aged_PD-1KO

source_name: CD8 T-cells from peripheral lymph node


title: Young_P3

value: CD44 high CD62Llow


title: Young_PD-1KO

value: 2 months old


title: Young_P4

value: CD44low CD62Llow


title: EC_DNA_AGM_cell301

tag: cell type

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)


title: EC_DNA_AGM_cell300

tag: tissue


title: EC_DNA_AGM_cell311

tag: strain


title: Aged_WT


title: Young_P2

value: CD44high CD62Lhigh


title: Young_WT with tumor


title: Young_PD-1KO with tumor


title: Aged_PD-1KO with tumor


title: RS3_Input_ Rep1

description: grown in a standard greenhouse


title: RS3_IP_ Rep2

description: grown in a standard greenhouse


title: RS3_IP_ Rep3

description: grown in a standard greenhouse


title: RS3_IP_ Rep1

description: grown in a standard greenhouse


title: EC_DNA_AGM_cell299

tag: antibody


title: EC_DNA_AGM_cell298


title: RS1_Input_ Rep3

description: grown in a standard greenhouse

source_name: Total RNA from RS1 fruit

value: 21 DPA


title: EC_DNA_AGM_cell297


title: EC_DNA_AGM_cell296


title: RS1_Input_ Rep2

description: grown in a standard greenhouse


title: RS1_Input_ Rep1

description: grown in a standard greenhouse


title: Young_WT


title: EC_DNA_AGM_cell295


title: RS1_IP_ Rep3

description: grown in a standard greenhouse


title: EC_DNA_AGM_cell294


title: RS1_IP_ Rep2

description: grown in a standard greenhouse


title: EC_DNA_AGM_cell293


title: EC_DNA_AGM_cell292


title: EC_DNA_AGM_cell290


title: EC_DNA_AGM_cell291


title: EC_DNA_AGM_cell289


title: EC_DNA_AGM_cell287


title: RS1_IP_ Rep1

description: grown in a standard greenhouse


title: S6_IP_ Rep2

description: grown in a standard greenhouse

source_name: Total RNA from S6 fruit

value: 15 DPA


title: S6_Input_ Rep1

description: grown in a standard greenhouse

value: Fruits with the removal of attached achenes


title: S6_IP_ Rep1

description: grown in a standard greenhouse


title: liver_pooled

city: Cambridge

first: Aviv

last: Regev

state: MA

address: 415 Main St

institute: The Broad Institute of MIT and Harvard

description: Single-cell or single nucleus RNA-Seq (10X). The count matrix is stored as an HDF5 file.

data_processing:
3' RNAseq (10x kit V2)
Demultiplexing is run using Cell Ranger mkfastq.
Cell Ranger count
Supplementary_files_format_and_content: Raw count matriece are in h5ad format, metadata files are comma-delimited text.

source_name: liver tissue tumor adjacent

extract_protocol:
We isolated single cells (using either liberase or collagenase A  dissociation) from subcutaneous adipose tissue collected from abdominoplasty surgery, and healthy liver tissue adjacent to tumor from liver resection
3' RNAseq (10x kit V2 chemistry)

value: liver

value: healthy


title: S6_IP_ Rep3

description: grown in a standard greenhouse


title: adipose_pooled

source_name: adipose tissue from abdominoplasty surgery

value: adipose


title: EC_DNA_AGM_cell284


title: EC_DNA_AGM_cell283


title: EC_DNA_AGM_cell282


title: EC_DNA_AGM_cell285


title: EC_DNA_AGM_cell280


title: EC_DNA_AGM_cell278


title: EC_DNA_AGM_cell277


title: S6_Input_ Rep3

description: grown in a standard greenhouse


title: EC_DNA_AGM_cell275


title: EC_DNA_AGM_cell274


title: EC_DNA_AGM_cell276


title: S6_Input_ Rep2

description: grown in a standard greenhouse


title: EC_DNA_AGM_cell273


title: EC_DNA_AGM_cell288


title: EC_DNA_AGM_cell272


title: EC_DNA_AGM_cell268


title: EC_DNA_AGM_cell270


title: EC_DNA_AGM_cell286


title: EC_DNA_AGM_cell269


title: EC_DNA_AGM_cell281


title: EC_DNA_AGM_cell267


title: EC_DNA_AGM_cell266


title: EC_DNA_AGM_cell264


title: EC_DNA_AGM_cell265


title: EC_DNA_AGM_cell261


title: EC_DNA_AGM_cell263


title: EC_DNA_AGM_cell260


title: EC_DNA_AGM_cell279


title: EC_DNA_AGM_cell258


title: EC_DNA_AGM_cell255


title: EC_DNA_AGM_cell257


title: EC_DNA_AGM_cell259


title: EC_DNA_AGM_cell254


title: EC_DNA_AGM_cell256


title: EC_DNA_AGM_cell253


title: EC_DNA_AGM_cell252


title: EC_DNA_AGM_cell249


title: EC_DNA_AGM_cell271


title: EC_DNA_AGM_cell251


title: EC_DNA_AGM_cell248


title: EC_DNA_AGM_cell247


title: EC_DNA_AGM_cell250


title: EC_DNA_AGM_cell246


title: EC_DNA_AGM_cell245


title: EC_DNA_AGM_cell262


title: EC_DNA_AGM_cell244


title: EC_DNA_AGM_cell243


title: EC_DNA_AGM_cell242


title: EC_DNA_AGM_cell240


title: EC_DNA_AGM_cell239


title: EC_DNA_AGM_cell238


title: EC_DNA_AGM_cell237


title: EC_DNA_AGM_cell234


title: EC_DNA_AGM_cell233


title: EC_DNA_AGM_cell232


title: Mia_NTC1_3

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

data_processing:
cut-adapt v1.2.1 to trim polyA tail and adapter seq 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
star version v2.5.3a for alignment
Genome_build: hg38
Supplementary_files_format_and_content: raw count table at the gene level for all 29 samples

molecule: polyA RNA

source_name: MiaPaCa2 cells

growth_protocol: DMEM basal media (Gibco) supplemented with high glucose, GlutaMax (Gibco), and penicillin/streptomycin

extract_protocol:
RNA was extracted with Total RNA Extration Kit with DNAse (Norgen)
QuantSeq 3_ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)
3' RNA-seq

treatment_protocol: MiaPaCa2 or Panc1 cells containg lentiMPHv2 plasmid were co-transfected with psPAX2, pMD2G, and lentiSAMv2 lentiviral plasmids containing NTC1, NTC2, or HDAC1 using Lipofecatming 2000 Transfection Reagent (ThermoFisher)

value: scrambeled non-targeting sgRNA

tag: replicate #


title: Mia_NTC1_2


title: Mia_NTC1_1


title: Mia_NTC2_3


title: EC_DNA_AGM_cell231


title: Mia_NTC2_2


title: EC_DNA_AGM_cell230


title: Mia_G10_SIN3B_B_SAM

value: SIN3B activation sgRNA


title: EC_DNA_AGM_cell227


title: Mia_G7_SIN3A_A_SAM

value: SIN3A activation sgRNA


title: EC_DNA_AGM_cell236


title: Mia_NTC2_1


title: EC_DNA_AGM_cell229


title: EC_DNA_AGM_cell228


title: EC_DNA_AGM_cell226


title: Saline

city: Bronx

first: Kosaku

last: Shinoda

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
Cell Ranger v3.0.2
Genome_build: refdata-cellranger-mm10-3.0.0 (10x Genomics)
Supplementary_files_format_and_content: filtered featured bc matrix

source_name: Inguinal Adipose Tissue

extract_protocol:
Adipose tissue is digested and enriched for the mature fraction. Adipocytes are then processed for nuclei isolation.
10X genomics snRNA-seq library construction protocol
snRNA-seq

value: Inguinal Adipose Tissue

value: Saline (5 days RT with injections, 5 days mild cold, with injections)


title: Mia_H5_ARID4A_A_SAM

value: ARID4A activation sgRNA


title: B-Blocker

value: B-blocker (5 days RT with injections, 5 days mild cold, with injections)


title: Mia_G11_SMARCA4_A_SAM

value: SMARCA4 activation sgRNA


title: EC_DNA_AGM_cell223

value: endothelial cells


title: EC_DNA_AGM_cell241

value: aorta-gonad-mesonephros (AGM)


title: Mia_E7_1_HDAC1_A_SAM

value: HDAC1 activation sgRNA


title: Mia_E7_3_HDAC1_A_SAM


title: Mia_G3_SAP18_A_SAM

value: MTA2 activation sgRNA


title: Mia_F11_RBBP7_A_SAM

value: SAP18 activation sgRNA


title: EC_DNA_AGM_cell235


title: WT

value: Cold acclimated followed by 1wk 6C

tag: genotype

value: WT


title: Mia_G6_SAP30_B_SAM

value: SAP30 activation sgRNA


title: Mia_F5_MTA2_A_SAM

value: RBBP7 activation sgRNA


title: Mia_E7_2_HDAC1_A_SAM


title: EC_DNA_AGM_cell224


title: EC_DNA_AGM_cell222


title: HL03- HKO LPS 6h, replicate 03

city: Los Angeles

first: Allison

middle: L

last: Fisher

state: CA

address: 650 Charles E Young Dr South, CHS 44-100

department: Medicine

institute: UCLA Center for Iron Disorders

data_processing:
Partek flow was used for bioinformatics methods.
The reads were mapped to the latest UCSC transcript set using STAR - 2.6.1d. The Partek E/M was used to quantify reads to an annotation model. After obtaining gene counts, the counts were normalized by TPM
The differential gene expressions were examined for "HKO vs. WT, baseline" and "HKO vs. WT, LPS 6h" using DESeq2 algorithm.
Genome_build: UCSC transcript set mm10
Supplementary_files_format_and_content: Text file matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Text file matrix table with normalized gene counts for every gene and every sample used for analysis of differentially expressed genes

source_name: Endothelial cells

extract_protocol:
Five placentas per pregnant dam were pooled and endothelial cells were isolated by magnetic separation using anti-CD31 magnetic beads on the MidiMACS system following the manufacturer's instructions (Miltenyi #130-095-927, #130-097-418). Total RNA was extracted using a RNeasy Micro kit (Qiagen #74004) following the manufacturer's instructions.
Strand-specific RNA-Seq libraries were generated using Nugen Universal plus mRNA-Seq Kit. The workflow consisted of poly(A) RNA selection, RNA fragmentation and double-stranded cDNA generation using a mixture of random and oligo(dT) priming, followed by end repair to generate blunt ends, adaptor ligation, strand selection, and PCR amplification to produce the final library.

treatment_protocol: WT and HKO mice received a single cubcutaneous injection of water or 0.5ug/g LPS O55:B5 on E15.5 for 6h prior to harvest.

value: Placenta

value: Endothelial cells

value: Hepcidin-1 KO

tag: development stage


title: HL04- HKO LPS 6h, replicate 04


title: EC_DNA_AGM_cell225


title: Panc1_NTC2_1

source_name: Panc1 cells

value: scrambeled non-targeting sgRNA


title: Panc1_NTC2_3


title: Mia_E5_GATA2_A_SAM

value: GATA2 activation sgRNA


title: Panc1_NTC2_2


title: HL02- HKO LPS 6h, replicate 02


title: Panc1_NTC1_2


title: HL01- HKO LPS 6h, replicate 01


title: EC_DNA_AGM_cell221

source_name: aorta-gonad-mesonephros (AGM)


title: UCP1 KO

value: Inguinal Adipose Tissue


title: Panc1_NTC1_3


title: Panc1_NTC1_1


title: EC_DNA_AGM_cell220


title: WL04- WT LPS 6h, replicate 04

value: Wildtype


title: Mia_E2_BRMS1_B_SAM

value: BRMS1 activation sgRNA


title: EC_DNA_AGM_cell218

value: endothelial cells


title: EC_DNA_AGM_cell217

value: aorta-gonad-mesonephros (AGM)


title: EC_DNA_AGM_cell219


title: EC_DNA_AGM_cell216


title: WT2 iPSC-derived neurons RNAseq

city: Nijmegen

first: Nael

last: Nadif Kasri

address: Geert Grooteplein Zuid 10

department: Department of Human Genetics

country: Netherlands

institute: Radboudumc

description:
E/I co-cultures (65/35) DIV49
Demultiplexed per sample barcode (Data processing step 3)

data_processing:
Base-calling using Illumina's bcl2fastq conversion
Reads in fastq file filtered for valid unique molecular identifier (UMI) and sample barcode
Fastq files split per sample based on sample barcode (allowing 1 bp mismatch per sample)
Trimming performed using Trimmomatic (version 0.33)
Mapping performed using STAR
Uniquely mapped reads selected
Duplicate reads removed using UMI-tools software package
Count matrices generated with HTSeq (version 0.9.1)
Raw counts transformed to log-transformed counts (logCPM) using edgeR (R package)
Genome_build: GRCh38.p12 (release 29, Ensembl 94)
Supplementary_files_format_and_content: Excel file with logCPM

source_name: excitatory/inhibitory neurons

extract_protocol:
RNA isolation performed with Quick-RNA Microprep kit (Zymo Research, R1051)
See methods section paper

tag: cell-type

value: iPSC-derived neurons

tag: e/i ratio

value: E/I co-cultures (65/35)

tag: days in vitro


title: WL03- WT LPS 6h, replicate 03


title: WL02- WT LPS 6h, replicate 02


title: Mia_E3_CHD4_A_SAM

tag: treatment

value: CHD4 activation sgRNA


title: WT1 iPSC-derived neurons RNAseq


title: WL01- WT LPS 6h, replicate 01


title: H04- HKO baseline, replicate 04


title: Panc1_E7_2_HDAC1_A_SAM

value: HDAC1 activation sgRNA


title: Panc1_E7_1_HDAC1_A_SAM


title: Panc1_E7_3_HDAC1_A_SAM


title: H03- HKO baseline, replicate 03


title: EC_DNA_AGM_cell214


title: EC_DNA_AGM_cell215


title: H01- HKO baseline, replicate 01


title: EC_DNA_AGM_cell213


title: H02- HKO baseline, replicate 02


title: IL13-/- IL-33 3

first: Melvin

last: Zhang

address: 1 Portland St.

department: Inflammation & Immunology

institute: Pfizer

description:
Gene-count-table.txt
Gene-fpkm-table.txt

data_processing:
QuickIsoSeq, which uses software below, was implemented to map the samples to a reference mouse genome.
Alignment tool: STAR_2.6.1d
Feature counts: subread-1.6.3
Base-calling: VarScan.v2.4.0
Tools to manipulate bam files: samtools-1.9
Quality control: RSeQC
Quantification of transcripts: QuickRNASeq; He et al., Methods in Molecular Biology, 2018.
Genome_build: GRCm38.primary.genome.fa
Supplementary_files_format_and_content: Count (Gene-count-table.txt) and FPKM (Gene-fpkm-table.txt) matrix files for genes and transcripts.

source_name: Spleen

extract_protocol:
Spleens were removed and RNA was harvested using RNeasy Mini Kit (Qiagen).
Libraries were prepared with the Illumina TruSeq Stranded mRNA Isolation protocol, pooled at equimolar concentration, and sequenced using the Illumina NextSeq 500.

treatment_protocol: Recombinant mouse IL-33 at 12.5 µg/kg or PBS vehicle was administered via i.p. injection every day for 1 week to WT or IL13-/- mice for a total of seven doses.

value: Spleen

value: 3-4 months


title: IL13-/- IL-33 2


title: IL13-/- IL-33 1


title: Oocyte High-fat Diet Sample 5

city: Shanghai

first: Yanchang Wei

last: Wei

address: #845 Lingshan Rd., Pudong New District, Shanghai 200135, China

institute: Shanghai Jiao Tong University

description: Oocyte H 5

data_processing:
The raw data is processed by the following steps to get clean reads: 1) Getting rid of low quality reads; 2) Getting rid of reads with 5' primer contaminants; 3) Getting rid of reads without 3' primer; 4) Getting rid of reads without the insert tag; 5) Getting rid of reads with poly A; 6) Getting rid of reads shorter than 18nt. Clean data is produced using software developed by BGI.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited fasta files include reads length, reads counts and reads sequence.

source_name: Oocytes

growth_protocol: Female F0 C57BL/6 mice were randomly assigned to a high-fat diet (45 kcal% fat; Research Diets, D12451) or control diet (10 kcal% fat; Research Diets, D12450H) from 9 to 16 weeks of age.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
For adaptor ligation, total RNA was mixed with 0.25 pM of 3’ adaptor, 33% polyethylene glycol (molecular weight 8000), 1× T4 ligase reaction buffer, 20 U RiboLock RNase Inhibitor (Thermo Fisher Scientific), and 40 U RNL 2tr K227Q (NEB) in a 10 μl reaction volume. After incubation at 22 °C for 2 hours, the samples were heated for inactivation at 75 °C for 5 min. Then 1 μl of 5 μM RT primer was added and the samples were used for 5’ adaptor ligation in a 15 μl reaction volume containing 5 pM of 5’ adaptor, 10 μM of adenosine triphosphate, 20 U of RiboLock RNase inhibitor (Thermo Fisher Scientific), and 10 U of T4 RNA ligase 1 (NEB) and incubated at 22 °C for 1 hour. For first-strand cDNA synthesis, 10 μl of ligation product was used as a template in a 20 μl RT reaction containing 2.5 μM of dNTP, 10 mM dithiothreitol, 20 U of RiboLock RNase inhibitor (Thermo Fisher Scientific), 200 U of M-MuLV Reverse Transcriptase (NEB), and 1× RT reaction buffer. The RT reaction was performed at 44 °C for 1 hour. PCR amplification was performed using high-fidelity DNA polymerase in a 50 μl reaction volume containing 1 U of KOD-Plus-Neo (TOYOBO), 5 μl of RT reaction product, 25 pM of RP1 primer, 25 pM of RPl primer, 1× PCR buffer 0.2 mM dNTPs, 1.5 mM MgSO4, and H2O. The PCR condition was: 94 °C 2 min, 22 repeats of (98 °C 10 s, 60 °C 30 s, 68 °C 15 s), and 4 °C hold. PCR products were gel purified by Poly-Gel DNA Extraction Kit (Omega Bio-Tek) according to the manufacturer’s instructions.

treatment_protocol: Maternal high-fat diet vs control, the oocyte small RNAs were analysed through small RNA sequencing.

value: Oocytes

value: 16 weeks


title: Oocyte High-fat Diet Sample 4

description: Oocyte H 4


title: EC_DNA_AGM_cell212


title: WT IL-33 3

value: WT


title: WT3 iPSC-derived neurons RNAseq


title: Oocyte High-fat Diet Sample 6

description: Oocyte H 6


title: EC_DNA_AGM_cell211


title: Oocyte High-fat Diet Sample 3

description: Oocyte H 3


title: W03- WT baseline, replicate 03

value: Placenta

value: Endothelial cells


title: WT IL-33 1


title: WT IL-33 2


title: EC_DNA_AGM_cell210


title: EC_DNA_AGM_cell208


title: W01- WT baseline, replicate 01


title: Oocyte Control Sample 6

description: Oocyte C 6


title: IL13-/- PBS 3

value: PBS


title: Oocyte Control Sample 5

description: Oocyte C 5


title: IL13-/- PBS 2


title: IL13-/- PBS 1


title: EC_DNA_AGM_cell207


title: IL-4-positive Lung 6 [LR_19; IonXpress_075]

city: Denver

first: Richard

middle: Lee

last: Reinhardt

state: Colorado

address: 1400 Jackson Street, K817A

department: Biomedical Research

institute: National Jewish Health

description:
processed data file:
139.19-09-18.S5XL-00648.bcmatrix.txt
144.21-09-18.S5XL-00648.bcmatrix.txt
145.21-09-18.S5XL-00648.bcmatrix.txt
RawCount_Matrix.txt
countNorm_Matrix.txt
vstNorm_Matrix.txt

data_processing:
Basecalling (Ion Torrent S5)
Alignment (Torrent mapping alignment program)
Quantification (Ion Torrent Ampliseq RNA plugin, unique mapping mode)
Count Normalizaiton (DESeq2)
VST Normalizaiton, blind = TRUE (DESeq2)
Genome_build: AmpliSeq Mouse Transcriptome V1 Reference (based on GRCm38)
Supplementary_files_format_and_content: Count matrices (Raw, Count Normalized, VST Normalized)

source_name: CD4 T cell from lung

extract_protocol:
CD4+ T cells were sorted into single cell suspensions and sample RNA was isolated using the Quick-RNA Microprep kit (Zymo Research) according to the manufacturer’s protocol.
Whole genome gene expression data was generated using the Ion Ampliseq Transcriptome Mouse Gene Expression Kit (ThermoFisher Scientific) with 2 nanograms of total RNA according the manufacturer’s protocol.

value: N. brasiliensis infection

tag: day post infecton

value: Day 9

value: Lung

value: CD4 T cell


title: EC_DNA_AGM_cell206

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)


title: IL4-negative lymph node 6 [LR_18; IonXpress_074]

source_name: CD4 T cells from mediastinal lymph node

value: Mediastinal lymph node

value: CD4 T cells


title: WT PBS 3


title: WT PBS 2


title: IL-4-negative Lung 6 [LR_20; IonXpress_076]


title: IL4-positive lymph node 6 [LR_17; IonXpress_073]


title: EC_DNA_AGM_cell205


title: W02- WT baseline, replicate 02

value: Wildtype


title: Oocyte High-fat Diet Sample 1

description: Oocyte H 1


title: W04- WT baseline, replicate 04


title: WT PBS 1

value: Spleen


title: Oocyte Control Sample 2

description: Oocyte C 2


title: EC_DNA_AGM_cell204


title: EC_DNA_AGM_cell209


title: IL-4-negative Lung 5 [LR_16; IonXpress_072]


title: 30_OB6CNT_Parabiosis_RNASeq [30_S45]

city: New York

first: Paul

middle: Vincent

last: Dellorusso

address: 701 West 168th Street, 724 Hammer Health Sciences Center

department: Genetics and Development

institute: Columbia University Irving Medical Center

data_processing:
Fastq files were ran through fastqc to check for sequencing quality. 5 of 35 samples (numbers 6, 15, 16, 27, 35) were omitted due to poor quality and / or low coverage. QC was visualized using MultiQC (Ewels et al Bioinformatics 2016)
Salmon (Patro et al Nature Methods 2017) was used to generate an index of the CHR Gencode mouse transcriptome (gencode.vM20.trasncripts.fa)
Salmon was used to quanitfy transcripts against the mouse transcriptome reference. Flags used were for automatic library type detection -l A (unstranded, single-end), --seqBias, --gcBias, and --validateMappings
Transcript quantification files (quants.sf) were convereted to gene level counts using TxImport (Soneson et al. F1000Research 2015)
Differential expresison on gene level counts was performed using DESeq2 (Love et al Genome Biology 2014). Results were generated using the lfcShrink and contrast functions, making pairwise comparsions on the indicated groups. Alpha threshold set to 0.05 and lfcThreshold to 1.
Genome_build: Read alignment was not utlized for this analysis. Gencode utilizes the GRCm38 primary assembly genome sequence as the reference for their transcriptome annotation.
Supplementary_files_format_and_content: Differential expression files include log2 fold changes generated by DESeq2 for each indicated comparison (with all samples from a given group identified by parabiont status utilized in the differential expression test). These files are listed as .csv files. A counts file is also provided with all the gene level counts for each sample that are used as the input for DESeq2, also as a .csv file.

source_name: Old B6 control

extract_protocol:
Hematopoietic stem cells were isolated from the bone marrow of mice through a standardized process of bone marrow extraction, creation of a single cell suspension, and flow cytometry based cell sorting. RNA was isolated using the PicoPure RNA Isolation Kit from ThermoFisher.
Purified RNA was used as input for the Nugen Ovation Trio low input RNA library preparation kit. Samples were processed on an automated robot system at the NYU Genome Technology Center

tag: age at procedure

value: 22 months old

tag: parabiont status

value: Old B6 control

tag: Sex

value: Male

value: Hematopoietic stem cells


title: Oocyte Control Sample 1

description: Oocyte C 1

value: Oocytes

tag: age

value: 16 weeks


title: EC_DNA_AGM_cell202


title: IL4-negative lymph node 5 [LR_14; IonXpress_070]


title: ESC_ATRXWT_BG4

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

data_processing:
Library strategy: CUT&Tag
The CUT&Tag reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured on gelatin-coated plates under standard conditions (KO-DMEM, 2mM Glutamax, 15% ES grade fetal bovine serum, 0.1mM 2-mercaptoethanol, 1x Pen/Strep, 1x NEAA and leukemia inhibitory factor).

extract_protocol:
CUT&Tag was performed as described (Kaya-Okur, H. S. et al). Briefly, nuclei were harvested and incubated with concanavalin A beads. The nuclei-beads were incubated with BG4 antibody, anti-DYKDDDK antibody, and anti-rabbit secondary antibody. The beads then incubated with pAG-Tn5 protein to pull down nuclei containing G4-Bg4 complex. The DNA was tagged adapeters by Tn5 under tagmentation. The tagged DNA was purified and PCR amplified with Nextera primers.
Libraries were constructed according to the reference (Kaya-Okur, H. S. et al).

tag: cell line

value: ESC

value: ATRX WT


title: ESC_ATRXKO_BG4

value: ATRX KO


title: Oocyte Control Sample 4

description: Oocyte C 4

tag: cell type


title: Oocyte Control Sample 3

description: Oocyte C 3


title: 29_OB6CNT_Parabiosis_RNASeq [29_S44]


title: ESC_ESETcKO_4OHT_ATAC_rep2

data_processing:
The ATAC-seq reads were aligned to the mm10 mouse reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Samples were prepared according to the Illumina Nextera protocol
Libraries were constructed according to the Illumina Nextera protocol.

value: unknown


title: IL4-positive lymph node 5 [LR_13; IonXpress_069]

value: N. brasiliensis infection

value: Day 9

tag: tissue


title: ESC_ESETcKO_4OHT_ATAC_rep1

tag: strain


title: 28_OB6CNT_Parabiosis_RNASeq [28_S43]


title: EC_DNA_AGM_cell200

data_processing:
Basecalls performed using CASAVA version 1.8.2.
For ChIP part, Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1) (ChIP part) and Hisat2 (version 2.0.4) (RNA part).
ChIP part:  Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard. RNA part: reads were counted by HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were aggregate bigwig files.

extract_protocol:
Following CoTECH protocol.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)

tag: antibody


title: 24_YB6CNT_Parabiosis_RNASeq [24_S39]

source_name: Young B6 control

value: 8-12 weeks

value: Young B6 control


title: EC_DNA_AGM_cell199


title: IL-4-negative Lung 4 [LR_12; IonXpress_068]

value: Lung

value: CD4 T cell


title: ESC_ESETcKO_DMSO_ATAC_rep2


title: IL-4-positive Lung 4 [LR_11; IonXpress_067]


title: 5_YB6CNT_Parabiosis_RNASeq [5_S22]


title: EC_DNA_AGM_cell203


title: EC_DNA_AGM_cell198


title: IL-4-positive Lung 5 [LR_15; IonXpress_071]


title: IL4-negative lymph node 4 [LR_10; IonXpress_066]

value: Mediastinal lymph node

value: CD4 T cells


title: 1_YB6CNT_Parabiosis_RNASeq [1_S18]

value: Male

value: Hematopoietic stem cells


title: EC_DNA_AGM_cell197


title: IL4-positive lymph node 4 [LR_9; IonXpress_065]


title: ESC_ATRXKO_K1562R_ATAC_rep2


title: 34_OISOB6_Parabiosis_RNASeq [34_S49]

source_name: Old isochornically parabiosed B6

value: 22 months old

value: Old isochornically parabiosed B6


title: EC_DNA_AGM_cell196


title: ESC_ATRXKO_K1562R_ATAC_rep1

value: ESC


title: EC_DNA_AGM_cell195


title: 32_OHETB6_Parabiosis_RNASeq [32_S47]

source_name: Old heterochronically parabiosed B6

value: Old heterochronically parabiosed B6


title: 33_YISOB6_Parabiosis_RNASeq [33_S48]

source_name: Young isochronically parabiosed B6

value: Young isochronically parabiosed B6


title: ESC_ATRXKO_L1238A_ATAC_rep2


title: EC_DNA_AGM_cell194


title: ESC_ATRXKO_L1238A_ATAC_rep1


title: IL-4-positive Lung 3 [LR_7; IonXpress_031]

value: N. brasiliensis infection


title: 31_YBJCNT_Parabiosis_RNASeq [31_S46]

source_name: Young BoyJ control

value: Young BoyJ control


title: ESC_ATRXKO_WT_ATAC_rep2


title: Oocyte High-fat Diet Sample 2

description: Oocyte H 2

value: Oocytes

value: 16 weeks


title: EC_DNA_AGM_cell193

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)


title: 26_OHETB6_Parabiosis_RNASeq [26_S41]


title: ESC_ESETcKO_DMSO_ATAC_rep1

value: unknown


title: IL4-negative lymph node 3 [LR_6; IonXpress_030]

value: Day 9


title: EC_DNA_AGM_cell192


title: ESC_ATRXKO_Ctl_ATAC_rep2


title: EC_DNA_AGM_cell201


title: IL-4-positive Lung 2 [LR_3; IonXpress_027]

value: Lung

value: CD4 T cell


title: ESC_ATRXKO_WT_ATAC_rep1


title: IL-4-negative Lung 2 [LR_4; IonXpress_028]


title: 25_YBJCNT_Parabiosis_RNASeq [25_S40]

value: 8-12 weeks

value: Male


title: 23_YISOB6_Parabiosis_RNASeq [23_S38]

value: Hematopoietic stem cells


title: ESC_ATRXKO_Ctl_ATAC_rep1


title: EC_DNA_AGM_cell190


title: EC_DNA_AGM_cell191


title: IL-4-negative Lung 3 [LR_8; IonXpress_032]


title: IL4-negative lymph node 2 [LR_2; IonXpress_026]

value: Mediastinal lymph node

value: CD4 T cells


title: EC_DNA_AGM_cell189


title: IL4-positive lymph node 3 [LR_5; IonXpress_029]


title: EC_DNA_AGM_cell188


title: 21_OISOB6_Parabiosis_RNASeq [21_S36]

value: 22 months old

value: Old isochornically parabiosed B6


title: EC_DNA_AGM_cell187


title: ESC_DAXXKO_EdU2h_rep2

data_processing:
Library strategy: EdU-seq
The EdU-seq reads were aligned to the mm10 mouse reference genome using Bowtie2 aligner.
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Edu-seq was performed as described (Macheret and Halazonetis 2019). Briefly, cell were fixed in 90% cold methanol and permeabilized with 0.2% Triton X-100/PBS for 30min. Edu-labeling cells were incubated with Click-it reaction mix (ThermoFisher, C10269). DNA was then sheared to 150-500 bp. Edu-labeling DNA was isolated and used for Edu-seq according to reference.
Libraries were constructed according to the Illumina Tru-seq protocol.

treatment_protocol: ESCs were synchronzied by thymidine 14h and nocodazol 7h. Mitotic cells were released in the medium with 10uM EdU prior 30min to collect cells for fixation. At releasing 2h, cells were harvested for downstream analysis.

value: ESC

value: DAXX-/-


title: IL-4-positive Lung other [GFP_plus_OTHER; IonXpress_093]

description:
processed data file:
124.18-04-18.S5XL-00648.bcmatrix.txt
RawCount_Matrix.txt
countNorm_Matrix.txt
vstNorm_Matrix.txt

source_name: non-T cell from lung

value: N. brasiliensis infection

value: non-T cell


title: IL4-positive lymph node 2 [LR_1; IonXpress_025]


title: ESC_ATRXKO_EdU2h_rep2

value: ATRX-/-


title: 20_YISOBJ_Parabiosis_RNASeq [20_S35]

source_name: Young isochronically parabiosed BoyJ

value: Young isochronically parabiosed BoyJ


title: ESC_WT_EdU2h_rep2

value: wildtype


title: ESC_WT_Input2h_rep1


title: EC_DNA_AGM_cell185

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)


title: EC_DNA_AGM_cell186


title: IL4-negative lymph node 1 [GFP_minus_CD4_LN; IonXpress_090]

value: Day 9


title: ESC_DAXXKO_EdU2h_rep1


title: 18_OBJCNT_Parabiosis_RNASeq [18_S33]

source_name: Old BoyJ cotnrol

value: 21 months old

value: Old BoyJ control


title: 17_YHETBJ_Parabiosis_RNASeq [17_S32]

source_name: Young heterochronically parabiosed BoyJ

value: 8-12 weeks

value: Young heterochronically parabiosed BoyJ

value: Male

value: Hematopoietic stem cells


title: 19_OISOBJ_Parabiosis_RNASeq [19_S34]

source_name: Old isochornically parabiosed BoyJ

value: Old isochornically parabiosed BoyJ


title: EC_DNA_AGM_cell184

source_name: aorta-gonad-mesonephros (AGM)


title: IL4-positive lymph node 1 [GFP_plus_CD4_LN; IonXpress_089]

value: Mediastinal lymph node

value: CD4 T cells


title: ESC_ATRXKO_EdU2h_rep1

value: ESC


title: ESC_WT_EdU2h_rep1


title: EC_DNA_AGM_cell183


title: 22_OISOB6_Parabiosis_RNASeq [22_S37]

value: 22 months old

value: Old isochornically parabiosed B6


title: 14_OHETB6X_Parabiosis_RNASeq [14_S30]

source_name: Old heterochronic B6 lodged in young BM niche


title: IL-4-positive Lung 1 [GFP_plus_CD4_Lung; IonXpress_091]

value: N. brasiliensis infection

value: Lung

value: CD4 T cell


title: EC_DNA_AGM_cell182

value: endothelial cells

value: aorta-gonad-mesonephros (AGM)


title: ESC_ATRXWT_GFP

data_processing:
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Crosslink ChIP was performed as described (Law et al. 2010; Truch et al. 2018). Briefly, cell were harvested and crosslinked in 2mM EGS for 45min and 1% PFA for 10min. Chromatin was then sheared to 150-500 bp. Chromatin was isolated and used for ChIP-seq according to standard procedures.
Libraries were constructed according to the Illumina Tru-seq protocol.

treatment_protocol: For genertating ATRX-GFP mouse ESCs, TagGFP2 were knocked-into the c-teminal of ATRX locus by CRISPR/Cas9-mediated homology directed repair. For generating ctrl, SSRP1 KD and SPT16 KD mouse ESCs, cells were infected with lentivirus containing non-targeting, SSRP1 and SPT16 shRNA plasmid (Dharmacon). The next day, the media was replaced with complete mESC culture media containing 1 μg/ml puromycin. After 3 days of selection, mESCs were used for downstream analysis.

value: wildtype

value: GFP (ab290, Abcam)

tag: ChIP

value: Crosslink


title: IL-4-negative Lung 1 [GFP_minus_CD4_Lung; IonXpress_092]

value: Day 9


title: 13_OISOB6_Parabiosis_RNASeq [13_S29]

value: Male


title: EC_DNA_AGM_cell181


title: ESC_ATRX-GFP_GFP

tag: genotype

value: ATRX-GFP


title: 11_OISOB6_Parabiosis_RNASeq [11_S27]

value: Hematopoietic stem cells


title: 12_OHETB6_Parabiosis_RNASeq [12_S28]

value: Old heterochronically parabiosed B6


title: EC_DNA_AGM_cell180


title: ESC_ATRXKO_ATRX

value: ATRX-/-

value: ATRX (ab97508, Abcam)


title: EC_DNA_AGM_cell179


title: EC_DNA_AGM_cell178


title: 10_YBJCNT_Parabiosis_RNASeq [10_S26]

value: 8-12 weeks

value: Young BoyJ control