title: talA_101412

city: Cambridge

first: Darren

middle: John

last: Parker

state: MA

address: 31 Ames Street

department: Biology

institute: MIT

data_processing:
Bam files were converted to fastq files using bedtools command bamtofastq
fastq files were stripped of polyA tail by finding and keeping sequence before first instance of 10 sequential A nt
Stripped fastq files were aligned to E. coli chromosome NC_000913.2 using bowtie with options -v 2 -k 1 --best
6 wig files per sample: 5' and 3' ends of reads counted singly for both strands (4 total). 'all' wig files count +1 for each nt of an aligning read to that chromosomal position
Genome_build: NC_000913.2
Supplementary_files_format_and_content: 6 wig files per sample: 5' and 3' ends of reads counted singly for both strands (4 total). 'all' wig files count +1 for each nt of an aligning read to that chromosomal position

organism: Bacillus subtilis

source_name: Bacillus subtilis

growth_protocol: Overnight cultures in MOPS Minimal Media (Teknova) were backdiluted 1:1000 into fresh media and grown to OD600 0.3 in shaking flasks at 37°C

extract_protocol:
Cells were mixed 1:1 with 50% Methanol and incubated on ice for 5 minutes before spin down for 10 minutes at 4°C. Methanol was removed, cells were lysed with lysozyme and RNA was purified using RNEasy kit as per manufacturers instruction (Qiagen)
RNA was fragmented (ThermoFischer #AM8740), dephosphorylated, polyadenlyated, and reverse transcribed using Superscript III and custom oligo-dT reverse transcription primers. Resulting cDNA was ligated with Illumina sequencing adapters and PCR amplified. Single end (50 bp) sequencing was performed on an Illumina HiSeq 2000.

tag: knockout

value: talA


title: tktB_101383

status: Public on Jul 11 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: strain

value: tktB


title: yhdL_101349

value: yhdL


title: surA_101382

value: surA


title: E8.25_heart_cell21

city: Beijing

first: Chen

last: Li

state: Beijing

address: Yihe Yuan Road No.5

department: Institute of Molecular Medicine

country: China

institute: Peking University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "-N 1".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad"
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bed files of non-duplicated reads.

molecule: genomic DNA

organism: Mus musculus

source_name: heart

growth_protocol: Mice were housed under a 12-12-hour light-dark cycle and allowed standard laboratory take care.

extract_protocol:
Crosslinked cells were treated with 0.3% SDS at 62°C. Transposition was set up by incubation at 55°C for 30 min, followed by addition of stopping buffer. Soluble chromatin was used for following ChIP experiments.  DNA was eluted from beads, reverse crosslinked and treated with proteinase K. Finally, DNA was extracted by pheno-chloroform.
After PCR enrichment using NEBNext Q5 Ultra II master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

tag: age

tag: cell type

value: heart cell

tag: chip antibody


title: stpA_101350

value: stpA


title: E8.25_heart_cell20


title: E8.25_heart_cell18


title: E8.25_heart_cell19


title: sufB_101416

value: sufB


title: sufC_101417

value: sufC


title: sufA_101385

value: sufA


title: speD_101411

value: speD


title: sodB_101345

value: sodB


title: E8.25_heart_cell13


title: spr_101381

value: spr


title: E8.25_heart_cell17


title: E8.25_heart_cell16


title: E8.25_heart_cell15


title: speB_101410

value: speB


title: speA_101409

value: speA


title: ha_170710A

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

description: processed data file: All_Embryo_TPM.txt

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling
scRNA-Seq:Read 2 was used to abtain the cell barcodes to further split the reads according to the cell IDs(barcode) and the same time recorded the UMI sequences;Read 1 was picked in each cell according to the cell ID in read2 and the UMI information was aligned to it,and then these raw reads were trimmed to remove TSO or polyA sequence;Adaptor contamination and low-quality reads were discarded from the trimmed Read 1 raw data;TopHat(version 2.0.14) with default settings were used for sequence alignment and uniquely mapped reads were kept.
Whole genome sequencing: Quality control pipeline was firstly performed on paired-end sequencing data to remove low quality reads. The cleaned reads were mapped to human genome (hg19) by BWA. The total sequence reads of each 10M window were calculated and normalized by the total read depth of each samples. For each 10M window, they were normalized by dividing the average reads depth of all samples. Finally, the CNV values were visualized by ggplot2 package.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: fresh embryo from IVF

extract_protocol:
After pick single cells using mouth pipette, they were transferred to cold scRNA-seq lysis buffer immediately. Subsequently, the lysis buffer were shocked for 3min at 72℃ to make sure the release of RNA.
We use a modified STRT protocol to construct our library. In brief, we use single cell-specific barcodes to insure the protocol was applicable to a large number of cells. After cDNA amplification, the single cells labeled with different barcodes as many as 48-96 cells can be pooled together for subsequent library construction and sequencing. What’s more, we add biotin in our indexed primers which can pair with 3’ cDNA primers, so after additional amplifying of pooled cDNAs following shearing to about 300bp , we use Dynabeads® MyOne™ Streptavidin C1 beads to enrich for the 3’. The RNA-seq library was constructed using a Kapa Hyper Prep Kit (Kapa Biosystems) and subjected to 150 bp paired-end sequencing on an Illumina HiSeq 4000 platform (sequenced by Novogene). Single cell whole-genome sequencing was carried out by using the MALBAC amplification technique. Briefly, the single cells dissociated from the individual embryo were picked by mouth pipette and put into the lysis buffer. The procedure of cell lysis includes the following two steps: 50 °C for 3 hr of incubation, and 70 °C for 15 min to inactivate the protease. The single cell genomic DNA products were subsequently used for quasilinear pre-amplification and the following exponential amplification step. Next, about 300bp long DNA fragments were generated by the Covaris S2 before the library construction with Kapa Hyper Prep Kit (Kapa Biosystems). The constructed libraries were sequenced on Illumina HiSeq 4000 platform, and paired-end 150-bp reads were obtained.
single cell RNA-Seq；single cell whole geneome sequencing

treatment_protocol: Base on in vitro culture system, human embryos of day6, day8, day10, day12, day14 were isolated and digested under the microscope (digested by accutase medium: 0.005% trypsin, 1:1, at 37℃ for 15-30min ). Single cells were washed by PBS (with 1% BSA) for at least three times. Then each individual cell was picked by mouth pipette.

tag: tissue

value: in vitro cultured post-implantation embryo

tag: tissue source

value: fresh embryo from IVF


title: E8.25_heart_cell14


title: E8.25_heart_cell12


title: smpB_101352

value: smpB


title: sodA_101344

value: sodA


title: slyD_101380

value: slyD


title: skp_101408

value: skp


title: sbp_101379

value: sbp


title: E8.25_heart_cell26

value: heart cell


title: E8.25_heart_cell9


title: E8.25_heart_cell8


title: E8.25_heart_cell7


title: rhlB_101387

value: rhlB


title: E8.25_heart_cell11


title: E8.25_heart_cell5


title: pykA_101342

value: pykA


title: pykF_101343

value: pykF


title: purT_101378

value: purT


title: E8.25_heart_cell2


title: E8.25_heart_cell3


title: E8.25_heart_cell10


title: E7.75_heart_cell191


title: E8.25_heart_cell1


title: E7.75_heart_cell190


title: poxB_101377

value: poxB


title: pfkB_101406

value: pfkB


title: E7.75_heart_cell189


title: ompF_101356

value: ompF


title: ppiD_101407

value: ppiD


title: nuoB_101405

value: nuoB


title: ompC_101355

value: ompC


title: E7.75_heart_cell186


title: E7.75_heart_cell188


title: msrB_101404

value: msrB


title: E7.75_heart_cell187


title: E7.75_heart_cell185


title: mltD_101375

value: mltD


title: E8.25_heart_cell6


title: metH_101403

value: metH


title: E8.25_heart_cell4


title: E7.75_heart_cell183


title: E7.75_heart_cell182


title: E7.75_heart_cell184


title: katE_101373

value: katE


title: katG_101402

value: katG


title: iscU_101415

value: iscU


title: E7.75_heart_cell180

value: heart cell


title: nlpD_101376

value: nlpD


title: E7.75_heart_cell179


title: iscS_101384

value: iscS


title: hchA_101401

value: hchA


title: E7.75_heart_cell177


title: E7.75_heart_cell176


title: hupA_101353

value: hupA


title: E7.75_heart_cell174


title: gpmM_101399

value: gpmM


title: grxB_101372

value: grxB


title: gshB_101400

value: gshB


title: gloA_101398

value: gloA


title: folX_101397

value: folX


title: E7.75_heart_cell172


title: fumA_101371

value: fumA


title: gdhA_101388

value: gdhA


title: E7.75_heart_cell181


title: E7.75_heart_cell169


title: fkpA_101396

value: fkpA


title: E7.75_heart_cell170


title: E7.75_heart_cell168


title: hupB_101354

value: hupB


title: fklB_101395

value: fklB


title: fis_101351

value: fis


title: E7.75_heart_cell175


title: E7.75_heart_cell178


title: E7.75_heart_cell166


title: E7.75_heart_cell165


title: E7.75_heart_cell163


title: E7.75_heart_cell171


title: E7.75_heart_cell167


title: deaD_101357

value: deaD


title: degP_101370

value: degP


title: fbaB_101394

value: fbaB


title: E7.75_heart_cell162

value: heart cell


title: cyoD_101368

value: cyoD


title: dacC_101369

value: dacC


title: E7.75_heart_cell161


title: cyoC_101367

value: cyoC


title: E7.75_heart_cell160


title: cyoB_101366

value: cyoB


title: E7.75_heart_cell159


title: cyoA_101365

value: cyoA


title: E7.75_heart_cell157


title: cspE_101348

value: cspE


title: E7.75_heart_cell156


title: cspC_101347

value: cspC


title: E7.75_heart_cell154


title: BW25113-WT_2-101386


title: E7.75_heart_cell155


title: BW25113-WT_1-101363


title: E7.75_heart_cell153


title: E7.75_heart_cell158


title: E7.75_heart_cell173


title: bcp_101364

value: bcp


title: E7.75_heart_cell151


title: E7.75_heart_cell150


title: asnB_101392

value: asnB


title: E7.75_heart_cell149


title: cspA_101346

value: cspA


title: E7.75_heart_cell152


title: E7.75_heart_cell148


title: argF_101390

value: argF


title: E7.75_heart_cell147


title: ahpF_101389

value: ahpF


title: ansB_101360

value: ansB


title: ahpC_101359

value: ahpC


title: E7.75_heart_cell145


title: acnA_101361

value: acnA


title: E7.75_heart_cell144


title: E7.75_heart_cell143


title: cueO_101393

value: cueO


title: E7.75_heart_cell141

value: heart cell


title: asnA_101362

value: asnA


title: aroG_101391

value: aroG


title: Dutch 500FG cohort, whole blood, individual s99

city: Groningen

first: Raul

last: Aguirre-Gamboa

address: Antonius Deusinglaan 1

department: Department of Genetics

country: Netherlands

institute: University of Groningen, University Medical Center Groningen

data_processing:
fastQ files were then trimmed for: low quality reads, adaptors and poly-A tails
Trimmed fastQ files were aligned to build human_g1k_v37 ensemble Release 75 reference genome, using hisat.
Aligned reads were sorted using SAMTools
Gene level quantification was performed using HTSeq-count
Genome_build: ensemble Release 75
Supplementary_files_format_and_content: Tab delimited file that contains the raw count table

source_name: whole blood expression

extract_protocol:
LabChip GX
TruSeq mRNA Sample prep kit

tag: disease state

value: healthy

tag: cohort

value: Dutch 500FG cohort

tag: Sex

value: female

value: whole blood


title: Dutch 500FG cohort, whole blood, individual s97

value: male


title: Dutch 500FG cohort, whole blood, individual s96


title: Dutch 500FG cohort, whole blood, individual s94


title: E7.75_heart_cell139


title: E7.75_heart_cell138


title: Dutch 500FG cohort, whole blood, individual s93


title: E7.75_heart_cell137


title: Dutch 500FG cohort, whole blood, individual s95


title: E7.75_heart_cell146


title: E7.75_heart_cell136


title: E7.75_heart_cell164


title: E7.75_heart_cell135


title: E7.75_heart_cell134


title: Dutch 500FG cohort, whole blood, individual s91


title: Dutch 500FG cohort, whole blood, individual s100


title: Dutch 500FG cohort, whole blood, individual s92


title: Dutch 500FG cohort, whole blood, individual s90


title: E7.75_heart_cell132


title: Dutch 500FG cohort, whole blood, individual s89


title: E7.75_heart_cell142


title: E7.75_heart_cell140


title: Dutch 500FG cohort, whole blood, individual s88


title: Dutch 500FG cohort, whole blood, individual s98


title: Dutch 500FG cohort, whole blood, individual s87


title: E7.75_heart_cell130


title: E7.75_heart_cell131


title: E7.75_heart_cell129


title: E7.75_heart_cell128


title: Dutch 500FG cohort, whole blood, individual s86


title: Dutch 500FG cohort, whole blood, individual s84


title: E7.75_heart_cell126


title: Dutch 500FG cohort, whole blood, individual s82


title: E7.75_heart_cell127


title: Dutch 500FG cohort, whole blood, individual s83


title: Dutch 500FG cohort, whole blood, individual s85


title: E7.75_heart_cell123


title: E7.75_heart_cell133


title: Dutch 500FG cohort, whole blood, individual s80


title: Dutch 500FG cohort, whole blood, individual s79


title: Dutch 500FG cohort, whole blood, individual s81


title: Dutch 500FG cohort, whole blood, individual s78


title: Dutch 500FG cohort, whole blood, individual s77


title: E7.75_heart_cell121


title: E7.75_heart_cell122


title: E7.75_heart_cell124


title: E7.75_heart_cell120


title: E7.75_heart_cell119


title: Dutch 500FG cohort, whole blood, individual s75


title: E7.75_heart_cell118


title: E7.75_heart_cell117


title: E7.75_heart_cell116


title: Dutch 500FG cohort, whole blood, individual s72


title: Dutch 500FG cohort, whole blood, individual s73


title: Dutch 500FG cohort, whole blood, individual s71


title: Dutch 500FG cohort, whole blood, individual s74


title: E7.75_heart_cell114


title: Dutch 500FG cohort, whole blood, individual s70


title: E7.75_heart_cell112


title: Dutch 500FG cohort, whole blood, individual s67


title: Dutch 500FG cohort, whole blood, individual s66


title: E7.75_heart_cell109


title: E7.75_heart_cell110


title: Dutch 500FG cohort, whole blood, individual s68


title: E7.75_heart_cell113


title: Dutch 500FG cohort, whole blood, individual s65


title: Dutch 500FG cohort, whole blood, individual s64


title: Dutch 500FG cohort, whole blood, individual s76


title: E7.75_heart_cell107


title: Dutch 500FG cohort, whole blood, individual s63


title: E7.75_heart_cell106


title: Dutch 500FG cohort, whole blood, individual s62


title: E7.75_heart_cell105


title: Dutch 500FG cohort, whole blood, individual s69


title: E7.75_heart_cell115


title: Dutch 500FG cohort, whole blood, individual s60


title: Dutch 500FG cohort, whole blood, individual s61


title: E7.75_heart_cell103


title: E7.75_heart_cell102


title: Dutch 500FG cohort, whole blood, individual s59


title: Dutch 500FG cohort, whole blood, individual s57


title: E7.75_heart_cell100


title: Dutch 500FG cohort, whole blood, individual s56


title: E7.75_heart_cell111


title: Dutch 500FG cohort, whole blood, individual s55


title: E7.75_heart_cell98


title: Dutch 500FG cohort, whole blood, individual s58


title: Dutch 500FG cohort, whole blood, individual s53


title: E7.75_heart_cell96


title: Dutch 500FG cohort, whole blood, individual s52


title: E7.75_heart_cell95


title: Dutch 500FG cohort, whole blood, individual s51


title: E7.75_heart_cell94


title: E7.75_heart_cell104


title: Dutch 500FG cohort, whole blood, individual s50


title: E7.75_heart_cell93


title: Dutch 500FG cohort, whole blood, individual s49


title: E7.75_heart_cell92


title: Dutch 500FG cohort, whole blood, individual s48


title: E7.75_heart_cell101


title: Dutch 500FG cohort, whole blood, individual s47


title: Dutch 500FG cohort, whole blood, individual s54


title: E7.75_heart_cell97


title: E7.75_heart_cell90


title: Dutch 500FG cohort, whole blood, individual s45


title: Dutch 500FG cohort, whole blood, individual s46


title: E7.75_heart_cell88


title: E7.75_heart_cell91


title: E7.75_heart_cell89


title: Dutch 500FG cohort, whole blood, individual s43


title: E7.75_heart_cell99


title: E7.75_heart_cell86


title: Dutch 500FG cohort, whole blood, individual s44


title: E7.75_heart_cell108


title: Dutch 500FG cohort, whole blood, individual s42


title: E7.75_heart_cell85


title: E7.75_heart_cell84


title: E7.75_heart_cell83


title: Dutch 500FG cohort, whole blood, individual s41


title: E7.75_heart_cell82


title: Dutch 500FG cohort, whole blood, individual s40


title: Dutch 500FG cohort, whole blood, individual s38


title: Dutch 500FG cohort, whole blood, individual s39


title: Dutch 500FG cohort, whole blood, individual s37


title: E7.75_heart_cell80


title: E7.75_heart_cell79


title: E7.75_heart_cell81


title: Dutch 500FG cohort, whole blood, individual s35


title: Dutch 500FG cohort, whole blood, individual s34


title: Dutch 500FG cohort, whole blood, individual s32


title: E7.75_heart_cell78


title: E7.75_heart_cell77


title: E7.75_heart_cell76


title: E7.75_heart_cell75


title: malT_101358

value: malT


title: E7.75_heart_cell74


title: Dutch 500FG cohort, whole blood, individual s30


title: Dutch 500FG cohort, whole blood, individual s31


title: E7.75_heart_cell73


title: E7.75_heart_cell72


title: Dutch 500FG cohort, whole blood, individual s29


title: E7.75_heart_cell125


title: E7.75_heart_cell71


title: E7.75_heart_cell87


title: Dutch 500FG cohort, whole blood, individual s36


title: Dutch 500FG cohort, whole blood, individual s27


title: E7.75_heart_cell70


title: Dutch 500FG cohort, whole blood, individual s25


title: Dutch 500FG cohort, whole blood, individual s26


title: E7.75_heart_cell69


title: E7.75_heart_cell68


title: Dutch 500FG cohort, whole blood, individual s28


title: Dutch 500FG cohort, whole blood, individual s24


title: E7.75_heart_cell66


title: Dutch 500FG cohort, whole blood, individual s23


title: Dutch 500FG cohort, whole blood, individual s22


title: E7.75_heart_cell65


title: Dutch 500FG cohort, whole blood, individual s20


title: E7.75_heart_cell63


title: Dutch 500FG cohort, whole blood, individual s21


title: E7.75_heart_cell64


title: E7.75_heart_cell61


title: E7.75_heart_cell60


title: E7.75_heart_cell62


title: Dutch 500FG cohort, whole blood, individual s19


title: Dutch 500FG cohort, whole blood, individual s18


title: E7.75_heart_cell59


title: E7.75_heart_cell58


title: Dutch 500FG cohort, whole blood, individual s17


title: E7.75_heart_cell57


title: Dutch 500FG cohort, whole blood, individual s15


title: Dutch 500FG cohort, whole blood, individual s14


title: E7.75_heart_cell56


title: Dutch 500FG cohort, whole blood, individual s16


title: Dutch 500FG cohort, whole blood, individual s13


title: genomic DNA_aorta_BAV_4

type: genomic

city: Shanghai

first: Sun

last: Pan

address: Fenglin Road 180

department: Department of Cardiac Surgery

institute: Zhongshan Hospital, Fudan University

description:
dilated aorta sample
Sample name: SAMPLE 39

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan system using standard recommended Illumina scanner setting

data_processing: genomestudio software V2011.1

label: Cy5 and Cy3

source_name: ascending aorta

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from aortic samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

value: ascending aorta

value: bicuspid aortic valve with ascending aorta dilation


title: EZH2_500_it_rep2_ESC

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "-N 1".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad"
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bigwig files. Bigwig files of replicates data could show the stability. Similarity among data of different cell magnitude reflected the applicability of itChIP-seq. H3K27me3-data and H3K4me4-data showed that signals could be detected in both active regions and repressed regions by itChIP.

source_name: cultured mESC (V6.5)

growth_protocol: Mouse embryonic stem cells were cultured in DMEM/F12 and neurobasal with 2i or 15% fetal bovine serum

extract_protocol:
Crosslinked cells were treated with 0.3% SDS at 37°C and followed by gentle sonication. Transposition was set up by incubation at 37°C for 1 h, followed by addition of stopping buffer. Soluble chromatin was used for following ChIP experiments.  DNA was eluted from beads, reverse crosslinked and treated with proteinase K. Finally, DNA was extracted by pheno-chloroform.
After PCR enrichment using NEBNext Q5 Ultra II master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

value: cultured mESC (V6.5)

tag: fixed by

value: formaldehyde

tag: molecule subtype

value: ChIP-DNA


title: genomic DNA_aorta_BAV_5

description:
dilated aorta sample
Sample name: SAMPLE 40

value: Male


title: genomic DNA_aorta_BAV_6

description:
dilated aorta sample
Sample name: SAMPLE 41


title: genomic DNA_aorta_BAV_3

description:
dilated aorta sample
Sample name: SAMPLE 37


title: Dutch 500FG cohort, whole blood, individual s11


title: E7.75_heart_cell55


title: EZH2_5K_it_rep2_ESC


title: genomic DNA_aorta_AD_7

description:
dissected aorta sample
Sample name: SAMPLE 15

value: aortic dissection


title: Dutch 500FG cohort, whole blood, individual s10


title: EZH2_500_it_rep1_ESC


title: genomic DNA_aorta_normal_6

description:
normal aortic sample
Sample name: SAMPLE 26

value: normal


title: genomic DNA_aorta_BAV_2

description:
dilated aorta sample
Sample name: SAMPLE 34


title: genomic DNA_aorta_normal_3

description:
normal aortic sample
Sample name: SAMPLE 17


title: Dutch 500FG cohort, whole blood, individual s33


title: genomic DNA_aorta_AD_4

description:
dissected aorta sample
Sample name: SAMPLE 7


title: EZH2_5K_it_rep1_ESC


title: genomic DNA_aorta_AD_5

description:
dissected aorta sample
Sample name: SAMPLE 8


title: PolII_5K_it_rep2_ESC


title: genomic DNA_aorta_AD_12

description:
dissected aorta sample
Sample name: SAMPLE 27


title: genomic DNA_aorta_AD_9

description:
dissected aorta sample
Sample name: SAMPLE 20


title: PolII_500_it_rep1_ESC


title: PolII_500_it_rep2_ESC


title: Dutch 500FG cohort, whole blood, individual s9


title: E7.75_heart_cell52

value: heart cell


title: Dutch 500FG cohort, whole blood, individual s8


title: genomic DNA_aorta_normal_5

description:
normal aortic sample
Sample name: SAMPLE 24


title: genomic DNA_aorta_AD_6

description:
dissected aorta sample
Sample name: SAMPLE 9


title: genomic DNA_aorta_AD_3

description:
dissected aorta sample
Sample name: SAMPLE 5


title: genomic DNA_aorta_normal_2

description:
normal aortic sample
Sample name: SAMPLE 13


title: genomic DNA_aorta_AD_8

description:
dissected aorta sample
Sample name: SAMPLE 18


title: PolII_5K_it_rep1_ESC


title: genomic DNA_aorta_AD_2

description:
dissected aorta sample
Sample name: SAMPLE 4


title: genomic DNA_aorta_BAV_1

description:
dilated aorta sample
Sample name: SAMPLE 30


title: E7.75_heart_cell50


title: E7.75_heart_cell51


title: Dutch 500FG cohort, whole blood, individual s7


title: P300_100_it_rep2_ESC

tag: ip reagent

value: bio-ChIP with SA beads


title: genomic DNA_aorta_AD_11

description:
dissected aorta sample
Sample name: SAMPLE 23


title: genomic DNA_aorta_AD_1

description:
dissected aorta sample
Sample name: SAMPLE 2


title: genomic DNA_aorta_normal_4

description:
normal aortic sample
Sample name: SAMPLE 21


title: P300_100_it_rep1_ESC


title: E7.75_heart_cell48


title: genomic DNA_aorta_normal_1

description:
normal aortic sample
Sample name: SAMPLE 1


title: Dutch 500FG cohort, whole blood, individual s5

value: healthy


title: P300_500_it_rep2_ESC


title: P300_500_it_rep1_ESC


title: P300_10K_it_rep1_ESC


title: genomic DNA_aorta_AD_10

description:
dissected aorta sample
Sample name: SAMPLE 22


title: E7.75_heart_cell47


title: E7.75_heart_cell49


title: Dutch 500FG cohort, whole blood, individual s6

value: Dutch 500FG cohort


title: H3K27me3_100_it_rep2_ESC


title: Dutch 500FG cohort, whole blood, individual s4


title: E7.75_heart_cell54


title: P300_10K_it_rep2_ESC


title: H3K27me3_100_it_rep1_ESC


title: Dutch 500FG cohort, whole blood, individual s2

value: female


title: E7.75_heart_cell45


title: E7.75_heart_cell43


title: E7.75_heart_cell46


title: Dutch 500FG cohort, whole blood, individual s12

value: whole blood


title: H3K27me3_10K_it_input_ESC

value: input-DNA


title: Dutch 500FG cohort, whole blood, individual s1

value: male


title: E7.75_heart_cell53


title: HEK293T-GFP-rep3

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description:
249F
GFP only
processed data: ABE_SECURE_counts.tsv

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh38/hg38) using STAR using a basic two-pass alignment strategy. Aligned reads were filtered for those reads that were uniquely mapping using the --outFilterMultimapNmax 1 flag.
Variants associated with BE treatment were called using the GATK best practices pipeline using GATK 3.8.1 and Picard 2.7.
No samples were excluded from bioinformatics analyses.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: ABE_SECURE_counts.tsv: Raw gene expression counts per gene estimated by STAR.

growth_protocol: HEK293T cells (CRL-3216, obtained from ATCC) were grown in culture using media consisting of DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco). Cells were used for experiments until passage 20 and passaged at ~80% confluency every 2-4 days to maintain an actively growing population and avoid anoxic conditions. Cells were tested for mycoplasma bi-weekly.

extract_protocol:
RNA was extracted with Macherey-Nagel’s NucleoSpin RNA Plus kit.
Illumina TruSeq Stranded Total RNA Gold, IDT-ILM unique dual indices for barcoding.

treatment_protocol: Transfections were performed using 50ug of transfection quality plasmid DNA (Qiagen Maxiprep) encoding desired ABEmax-P2A-EGFP or bpNLS-32AAlinker-nCas9-bpNLS-P2A-EGFP and gRNAs (nuclease-to-gRNA ratio 75:25%). 7x10E6 HEK293T were seeded into TC-treated 150mm plates 18-24h prior to transfection to yield ~60-80 % confluency on the day of transfection. Cells were transfected using 150uL TransIT-293 (HEK293T, Mirus) reagents per plate, according to the manufacturers’ protocols (mixing DNA and reagent in 5mL Optimem, 30min incubation). Cells were sorted 36-40h after transfection, for all GFP signal after doublet-exclusion and gating for the cell population on a BD FACSARIA II.

tag: cell line

tag: treatment

tag: guide rna

tag: gfp

value: All GFP


title: E7.75_heart_cell41

tag: strain


title: P1 without CpG

type: RNA

city: PAris

first: Maxime

last: Touzot

address: 26 rue d'ULM

country: France

institute: Institut Curie

hyb_protocol: Labelled DNA was hybridized on whole human genome chips (HumanHT-12 Expression BeadChip Kit, Illumina)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Illumina)

data_processing: The bioinformatics analysis and normalization were performed using GeneSpring GX 7.3 (Agilent, Palo Alto, CA). Probes with an expression lower than 100 Units were filtered out. Data are expressed in log base 2. Differential gene expression was defined according to the two following criteria: Fold Change > 2; p-value < 0.05 (T-test).

label: biotin

source_name: Patient 1 treated without CpG

label_protocol: For each condition, 100 ng of RNA was  amplified and labeled to produce cDNA

growth_protocol: CD19+CD27+IgM+IgD-/low memory B cells were stimulated or not with CpG (Sigma 2.5ng/ml) For 72 hours  in 48-well plates (Falcon) at a density of 10^5cells per well.

extract_protocol: RNA was extracted using NuceloSpin RNA Kit II

value: IgM memory B cells


title: H3K27ac_500_it_ESC_truseq


title: Dutch 500FG cohort, whole blood, individual s3

tag: age


title: E7.75_heart_cell42

tag: cell type


title: H3K27me3_10K_it_rep1_ESC

tag: chip antibody


title: HEK293T-ABEsite16-miniABEmax_variant2-rep3

description:
249E
miniABEmax(V82G)
processed data: ABE_SECURE_counts.tsv

value: ABEsite16 guide:GGGAATAAATCATAGAATCC


title: 4765_12_DU145-OE_Double_ATTCCT_S41_R1_001.fastq.gz

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

institute: Netherlands Cancer Institute (NKI)

data_processing:
RNA-seq:Sequenced reads were aligned to the human genome (hg19) using TopHat v2.0.8 (Trapnell et al, 2009). Only uniquely mapped reads were retained for further analysis. SAMTOOLS v0.1.19 (Li et al, 2009) was used to convert the BAM output to SAM format and to sort the BAM file. The read counts per gene were calculated using the HTSeq program, v0.5.4p1 (Anders et al, 2015). The DESeq package (Oshlack et al, 2010) was used to generate normalized read counts and for differential gene expression analysis.  DESeq called differentially expressed genes with FDR cutoff of 0.05 and abs (FC) >1.5 were considered as significant differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: read counts per gene

source_name: DU145-SLC1A3oe cells

extract_protocol:
CRISPR-Cas9 screen: Genomic DNA was isolated using the phenol-chloroform extraction protocol and sgRNAs were amplified using a two-step PCR protocol for next-generation sequencing. RNA-seq: Total RNA was isolated using Trisure reagent (Bioline) following the manufacturer’s instructions. Briefly, cells were washed twice with PBS and 1 ml Trisure was added for homogenization. After centrifuge, the aqueous phase was transferred to a new tube and mixed with cold isopropyl alcohol for RNA precipitation by centrifuging at 4 °C for 1 hour. RNA pellet was washed twice with 75% ethanol and finally dissolved in RNase-free water.
RNA-seq: Stranded-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina) following the manufacturer’s instructions. Briefly, 2 mg of total RNA was polyA-selected using oligo-dT beads and the RNA was fragmented, random primed and reverse transcribed using SuperScript II Reverse Transcriptase kit (Invitrogen). Second strand complementary DNA was then synthesized, 3’-adenylated and ligated to Illumina sequencing adapters, and subsequently amplified by 12 cycles of PCR. The sequencing libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent) and pooled equimolarly into a 30 nM multiplex sequencing pool.

tag: tissue

value: Prostate

value: Prostate cancer cells

value: ASNase+TFB-TBOA


title: E7.75_heart_cell44


title: H3K27me3_10K_it_rep2_ESC

value: cultured mESC (V6.5)

value: formaldehyde

value: ChIP-DNA


title: H3K4me3_agg192_it_exp3_EpiLC

source_name: cultured EpiLC

value: cultured EpiLC


title: E7.75_heart_cell40

value: heart cell


title: 4765_11_DU145-OE_inhi_ACTGAT_S40_R1_001.fastq.gz

value: TFB-TBOA


title: 4765_9_DU145-OE_Ctrl_CGTACG_S38_R1_001.fastq.gz

value: Control


title: HEK293T-ABEsite16-miniABEmax_variant1-rep3

description:
249D
miniABEmax(K20A+R21A)
processed data: ABE_SECURE_counts.tsv


title: P3 without CpG

source_name: Patient 3 treated without CpG


title: P2 with CpG

source_name: Patient 2 treated with CpG


title: P2 without CpG

source_name: Patient 2 treated without CpG


title: P1 with CpG

source_name: Patient 1 treated with CpG


title: 4765_8_DU145_Double_GTTTCG_S37_R1_001.fastq.gz

source_name: DU145 cells


title: H3K4me3_agg96_it_exp1_EpiLC


title: E7.75_heart_cell38


title: HEK293T-ABEsite16-ABEmax-rep3

description:
249B
ABEmax
processed data: ABE_SECURE_counts.tsv


title: 4765_7_DU145_Inhi_GTGGCC_S30_R1_001.fastq.gz


title: 4765_10_DU145-OE_ASNase_GAGTGG_S39_R1_001.fastq.gz

value: ASNase


title: HEK293T-ABEsite16-control-rep3

description:
249A
nCas9
processed data: ABE_SECURE_counts.tsv


title: E7.75_heart_cell37


title: H3K4me3_500_it_soni60s_rep1_ESC


title: E7.75_heart_cell36


title: H3K4me3_agg192_it_exp2_EpiLC


title: HEK293T-ABEsite16-miniABEmax-rep3

description:
249C
miniABEmax
processed data: ABE_SECURE_counts.tsv


title: H3K4me3_500_it_soni30s_rep1_ESC


title: HEK293T-GFP-rep2

description:
248F
GFP only
processed data: ABE_SECURE_counts.tsv


title: E7.75_heart_cell35


title: HEK293T-ABEsite16-miniABEmax_variant2-rep2

description:
248E
miniABEmax(V82G)
processed data: ABE_SECURE_counts.tsv


title: E7.75_heart_cell34


title: H3K4me3_500_it_soni30s_rep2_ESC


title: 4765_5_DU145_Ctrl_TAGCTT_S35_R1_001.fastq.gz


title: H3K4me3_500_it_soni60s_rep2_ESC


title: HEK293T-ABEsite16-miniABEmax_variant1-rep2

description:
248D
miniABEmax(K20A+R21A)
processed data: ABE_SECURE_counts.tsv


title: H3K4me3_500_it_soni0s_rep2_ESC


title: E7.75_heart_cell33


title: P3 with CpG

source_name: Patient 3 treated with CpG


title: 4765_4_PC3_Double_GATCAG_S34_R1_001.fastq.gz

source_name: PC3 cells


title: 4765_3_PC3_Inhi_ACTTGA_S33_R1_001.fastq.gz


title: HEK293T-ABEsite16-miniABEmax-rep2

description:
248C
miniABEmax
processed data: ABE_SECURE_counts.tsv


title: H3K4me3_500_it_soni0s_rep1_ESC


title: 4765_2_PC3_ASNase_TTAGGC_S32_R1_001.fastq.gz


title: HEK293T-ABEsite16-ABEmax-rep2

description:
248B
ABEmax
processed data: ABE_SECURE_counts.tsv


title: H3K4me3_500_it_EpiLC


title: 4765_6_DU145_ASNase_GGCTAC_S36_R1_001.fastq.gz


title: E7.75_heart_cell32


title: 4765_1_PC3_Ctrl_ATCACG_S31_R1_001.fastq.gz


title: E7.75_heart_cell30


title: HEK293T-ABEsite16-control-rep2

description:
248A
nCas9
processed data: ABE_SECURE_counts.tsv


title: HDAC2_697

first: Chi-Shuen

last: Chu

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 (v2.3.2.2) with default parameters
Peaks were called using Homer (v4.9.1) with the default setting for factors.
Peaks were filtered for significance (p-value < 1.00E-10)
Peaks were annotated using Homer (v4.9.1) with the default setting
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files were generated using Homer (v4.9.1).

source_name: pre-B cell line

growth_protocol: 697 cells were routinely cultured by re-plating d 3 suspension cultures with RPMI-1640 supplemented with 10% fetal bovine serum and 1% of P/S

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3" to 5" exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were size selected and purified by Agencourt Ampure XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: HDAC2 (Abcam, ab7029)


title: H3K4me3_100_it_rep2_ESC


title: HEK293T-GFP-rep1

description:
247F
GFP only
processed data: ABE_SECURE_counts.tsv


title: E7.75_heart_cell29


title: E7.75_heart_cell28


title: HEK293T-ABEsite16-miniABEmax_variant1-rep1

description:
247D
miniABEmax(K20A+R21A)
processed data: ABE_SECURE_counts.tsv


title: E7.75_heart_cell27


title: E7.75_heart_cell26


title: HEK293T-ABEsite16-miniABEmax_variant2-rep1

description:
247E
miniABEmax(V82G)
processed data: ABE_SECURE_counts.tsv


title: HEK293T-ABEsite16-miniABEmax-rep1

description:
247C
miniABEmax
processed data: ABE_SECURE_counts.tsv


title: E7.75_heart_cell25


title: HEK293T-ABEsite16-ABEmax-rep1

description:
247B
ABEmax
processed data: ABE_SECURE_counts.tsv


title: MTA2_697

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 (v2.3.2.2) with default parameters
Peaks were called using Homer (v4.9.1) with the default setting for factors.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files were generated using Homer (v4.9.1).

tag: chip antibody catalog/vendor

value: ab8106, Abcam

tag: antibody


title: Mi2_697

value: ab72418, Abcam


title: OCAB_697

value: sc-955, Santa Cruz

value: OCAB


title: E7.75_heart_cell39


title: E7.75_heart_cell23


title: H3K4me3_100_it_rep1_ESC


title: HEK293T-ABEsite16-control-rep1

description:
247A
nCas9
processed data: ABE_SECURE_counts.tsv

value: ABEsite16 guide:GGGAATAAATCATAGAATCC

value: All GFP


title: E7.75_heart_cell24


title: INPUT_697


title: AIOLOS_697

value: ab139408, Abcam

value: AIOLOS


title: OCT2_697

value: sc233, Santa Cruz


title: E7.75_heart_cell22


title: IKAROS_697

value: ab26083, Abcam

value: IKAROS


title: HEK293T-HEKsite2-miniABEmax_variant2-rep3

description:
246E
miniABEmax(V82G)
processed data: ABE_SECURE_counts.tsv

value: HEKsite2 guide:GAACACAAAGCATAGACTGC


title: HEK293T-HEKsite2-miniABEmax_variant1-rep3

description:
246D
miniABEmax(K20A+R21A)
processed data: ABE_SECURE_counts.tsv


title: E7.75_heart_cell18

value: heart cell


title: neuronal stem cells differentiated from ND41658*H cell line,biol. rep 2

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Gene expression data from LnCap cell line

hyb_protocol: Biotin-labeled miRNA were hybridized to Applied Biosystems™ miRNA 4.1 Array Strip (20 h, 48 °C). Then, the microarrays were subjected to a washing and staining procedure, according to the technical protocol, using the Affymetrix GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The array strips were scanned using an Imaging Station of GeneAtlas System (Thermo Fisher Scientific, MA, USA). The preliminary analysis of the scanned chips was carried out by means of Affymetrix GeneAtlas Operating Software (Affymetrix, Santa Clara, CA, USA).

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

source_name: ND41658*H cell line

label_protocol: The complete procedure for preparing miRNA for hybridization was performed using the FlashTagTM Biotin HSR RNA Labeling Kit (ThermoFisher Scientific, Waltham, MA, USA). 150 ng of previously isolated miRNA was subjected to poly(A) tailing and biotin ligation procedure, according to producer protocol.

growth_protocol: GPCCi001-A and ND41658*H cell lines were cultured on Matrigel™coated plates in Essential 8 medium (Thermo Fisher Scientific) at 37°C in a 5% O2 and 5% CO2 mixture. NSC derived from GPCCi001-A cells were cultured in Neural Expansion Medium (consisting of 1:1 mixture of Neurobasal Medium : DMEM F-12 and 1x Neural ® Induction Supplement, Thermo Fisher Scientific). NSC derived from ND41658*H cells were cultured in STEMdiff™ Neural Progenitor Basal Medium supplemented with 2x Supplement A and 0,1x Supplement B (Stemcell Technologies, Vancouver, Canada) on Geltrex™ coated plates (1:25 solution)

extract_protocol: Total RNA with miRNA was purified with TRI Reagent solution and with miRNeasy Kit and RNeasy MinElute kits.

treatment_protocol: Differentiation of GPCCi001-A cell line (generated and characterized in our laboratory [21]) was performed with one-step monolayer culture protocol. iPSC were seeded onto a six-well culture plate coated with Matrigel (1:20 solution) with a confluence less than 20%. Differentiation was performed in Neural Induction Medium consisting of Neurobasal Medium (Gibco, Waltham, MA, USA) supplemented with 1x Neural ® Induction Supplement (Gibco, Waltham, MA, USA).   Differentiation of commercially available ND41658*H iPSC (Coriell Cell Repository, NY, USA) iPSC cell line was also performed with one step monolayer culture, however using a STEMdiff™ Neural Induction Medium supplemented with STEMdiff™ SMADi Neural Induction Supplement and 10 µM Y-27632 (Stemcell Technologies, Vancouver, Canada).

value: Neural stem cells differentiated from human induced pluripotent stem cell (NSC)


title: Yersinia_exp

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter ATCTCGTATGCCGTCTTCTGCTTG and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using bowtie2 -t --phred64 -N 0 -p 24. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01 Qvalue <= 0.05
Genome_build: Yersinia pestis biovar Microtus 91001
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

organism: Yersinia pestis

source_name: Bacterial strain

growth_protocol: Bacteria were grown in brain heart infusion (BHI) broth (Difco) supplemented with appropriate antibiotics overnight at 26 °C with shaking at 200 rpm until exponential growth phase (OD620 = 0.8).

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using SmartSpec Plus (BioRad). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
A total of 2.5μg of total RNA was used for cDNA library preparation with the adaptors accordance to illumina protocol. Briefly, RNAs were ligated to 3' and 5' adaptor sequentially and reverse transcribed to cDNA and then PCR amplified (RNA 3' Adapter: /5rApp/ATCTCGTATGCCGTCTTCTGCTTG/3’NH2/, RNA 5' Adapter 5’GUUCAGAGUUCUACAGUCCGACGAUCNNN3’). Whole library was applied to 10% native PAGE gel electrophoresis and bands corresponding to 80-380 bp RNA insertion were cut and eluted.

treatment_protocol: Bacterial growth was stopped by centrifugation for 6 min at 5,000 rpm at 4 °C. The pellets were frozen into liquid nitrogen and stored at -80 °C until cells were lysed. Western blotting was performed by using monoclonal FLAG antibody (Sigma) to detect the Flag-tagged proteins.

value: wild-type strain 201 carrying pACYC184-Hfq-Flag


title: H3K27ac_500_it_ESC

value: cultured mESC (V6.5)

value: formaldehyde

value: ChIP-DNA


title: neuronal stem cells differentiated from GPCCi001-A cell line,biol. rep 2

source_name: GPCCi001-A cell line, differentiated to neuronal stem cells


title: HEK293T-HEKsite2-ABEmax-rep3

description:
246B
ABEmax
processed data: ABE_SECURE_counts.tsv


title: undifferentiated GPCCi001-A cell line, biol. rep 2

source_name: GPCCi001-A cell line, served as control

value: Human induced pluripotent stem cell (hiPSC)


title: HEK293T-HEKsite2-control-rep3

description:
246A
nCas9
processed data: ABE_SECURE_counts.tsv


title: neuronal stem cells differentiated from ND41658*H cell line,biol. rep 1


title: HEK293T-HEKsite2-miniABEmax-rep3

description:
246C
miniABEmax
processed data: ABE_SECURE_counts.tsv


title: undifferentiated ND41658*H cell line, biol. rep 2


title: neuronal stem cells differentiated from GPCCi001-A cell line,biol. rep 1


title: undifferentiated ND41658*H cell line, biol. rep 1


title: Adult mouse brain cortex, rep 12, RNA-seq

city: La Jolla

first: Song

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

description:
2-month-old adult mouse
processed data file: Ad_BrainCortex_SNAREseq_cDNA.counts.mtx
processed data file: Ad_BrainCortex_SNAREseq_cDNA.genes.tsv
processed data file: Ad_BrainCortex_SNAREseq_cDNA.barcodes.tsv

data_processing:
Basecalls performed using bcl2fastq v2.17
Reads with less than five T bases in the last nine bases of read 1 or a poor quality score (<10) were filtered out
Cell barcode and UMI information were inferred from the first 20 bases of read 1.
STAR v2.5 was used to align cDNA reads with reference genome.
Encode ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines) was used to trim and call peaks with paired-end chromatin reads as input.
Peak files were converted to Picard style interval_list file and overlapped with each mapped reads to assign reads with peak region.
Digital accessibility matrix or expression matrix was then generated with peak region or gene name as rows and cell barcodes as columns.
Genome_build: mm10
Supplementary_files_format_and_content: Sparse matrix with expression and accessibility counts values and tab-delimited text files showing barcodes and gene/peak names files for mouse brain cortex experiment.

source_name: mouse brain

extract_protocol:
Nuclei were extracted from adult mouse brain cortex by Nuclei EZ Prep kit.
RNA libraries were prepared for sequencing using standard Dropseq protocol. ATAC-seq libraries were prepared by amplifying beads captured chromatin fragments with dropseq P5_Tso and nextera index1 primers and gel size-selected for bands in the range of 225 bp and 1000 bp.

value: brain

tag: developmental stage

value: Adult (2 months)

tag: type

value: Nuclei


title: HEK293T-HEKsite2miniABEmax_variant2-rep2

description:
245E
miniABEmax(V82G)
processed data: ABE_SECURE_counts.tsv

value: All GFP


title: E7.75_heart_cell16

source_name: heart


title: undifferentiated GPCCi001-A cell line, biol. rep 1


title: Adult mouse brain cortex, rep 11, RNA-seq


title: E7.75_heart_cell15


title: Adult mouse brain cortex, rep 10, RNA-seq


title: Yersinia_kong

value: wild-type strain 201 carrying pACYC184-Flag


title: HEK293T-HEKsite2-miniABEmax_variant1-rep2

description:
245D
miniABEmax(K20A+R21A)
processed data: ABE_SECURE_counts.tsv


title: Broth 1

city: Glasgow

first: Tom

last: Evans

state: Glasgow

address: 120 University Avenue

department: Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

description:
Todd Hewitt Broth
Table_S3.xlsx

data_processing:
Basecalls generated with Illumina Hiseq software
Adaptors trimmed with Cutadapt and Sickle
Reads aligned to references using CLC Genomics Workbench
Genome_build: Mouse GRCm38; pneumococcus NC_017592
Supplementary_files_format_and_content: Excel spread sheet with reads mapped per gene ID
Supplementary_files_format_and_content: Table_S3.xlsx: gene counts bacteria
Supplementary_files_format_and_content: Table_S4.xlsx: gene counts mouse

organism: Streptococcus pneumoniae

source_name: Broth culutre of SRL1

extract_protocol:
Samples in Trizol with Zirconia beads from the animal model of infection were vortexed for 10 minutes to ensure complete lysis. Bacteria were also grown to mid-log phase in broth and processed in identical fashion. 1.33 ml of chloroform was added to each tube before vigorous shaking and incubation for 10 minutes at room temperature. Samples were then centrifuged at 8,000 g for 15 minutes at 4°C and the aqueous phase removed with a Pasteur pipette. RNA was extracted using the Zymo RNA clean and concentrator kit (Zymo Research) according to the manufacturer’s instructions. Further purification was performed with Agencourt RNAClean XP beads (Beckman Coulter). Ribosomal RNA was depleted using the Ribo-Zero rRNA removal kit (Illumina) according to the manufacturer’s instructions. RNA concentration and quality were assessed using the Agilent 2100 Bioanalyser.
Strand specific ScriptSeq library prep kit (Illumina)

value: Bacteria


title: Broth 2

description:
Todd Hewitt Broth
Table_S3.xlsx


title: Broth 3

description:
Todd Hewitt Broth
Table_S3.xlsx


title: HEK293T-HEKsite2-miniABEmax-rep2

description:
245C
miniABEmax
processed data: ABE_SECURE_counts.tsv


title: E7.75_heart_cell14


title: E7.75_heart_cell21


title: Adult mouse brain cortex, rep 9, RNA-seq


title: E7.75_heart_cell12


title: Yersinia_ctrl

value: wild-type strain 201


title: HEK293T-HEKsite2-ABEmax-rep2

description:
245B
ABEmax
processed data: ABE_SECURE_counts.tsv


title: E7.75_heart_cell17


title: Adult mouse brain cortex, rep 7, RNA-seq


title: HEK293T-HEKsite2-miniABEmax_variant2-rep1

description:
244E
miniABEmax(V82G)
processed data: ABE_SECURE_counts.tsv


title: E7.75_heart_cell11


title: fpr3fpr4

city: Victoria

first: Chris

last: Nelson

state: BC

address: 3800 Finnerty Road

department: Dept. of Biochemistry & Microbiology, The University of Victoria

country: Canada

institute: University of Victoria

description: ribo-minus  RNA

data_processing:
Wig files:Wiggle file generation using BAM2WIG tool (http://www.epigenomes.ca/tools-and-software)
TPM: TPM (Transcripts Per Kilobase Million) calculation using ss4v90 Ensembl gene models. Custom pipeline using the following steps: 0. Count reads falling in each gene genomic estate. 1. Divide the read counts by the length of each gene in kilobases. This gives you reads per kilobase (RPK).  2. Count up all the RPK values in a sample and divide this number by 1,000,000. This is your “per million” scaling factor.  3. Divide the RPK values by the “per million” scaling factor. This gives TPM.
Genome_build: sacSer3 (Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database (GCA_000146055.2))
Supplementary_files_format_and_content: Wig files: UCSC wiggle file format, gzipped. We generated two wig files for every sample corresponding to cDNA for positive and negative strand
Supplementary_files_format_and_content: TPM:  Each file contains gene information (gene_id,chr,start,end,strand, gene_type,  gene_name),  read_counts and TPM values.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were grown to mid-log phas in YPD media.

extract_protocol:
Total RNA was extracted using the phenol-freeze method.
RNAs were ribo-depleated using the Ribo-Zero Gold rRNA Removal Kit (Yeast) (Illumina) and analyzed on an Agilent 2100 Bioanalyzer using Agilent 6000 RNA Nano Kit (Agilent Technologies, Santa Clara, California). cDNA was generated using the Superscript Double-Stranded cDNA Synthesis kit (ThermoFisher), 100bp paired-end libraries prepared using the Paired-End Sample Prep Kit (Illumina, San Diego, California).

tag: genotype

tag: growth phase

value: mid log phase


title: trf5fpr3

description: ribo-minus  RNA


title: trf5fpr3fpr4

description: ribo-minus  RNA


title: E7.75_heart_cell9


title: fpr4

description: ribo-minus  RNA


title: HEK293T-HEKsite2-miniABEmax_variant1-rep1

description:
244D
miniABEmax(K20A+R21A)
processed data: ABE_SECURE_counts.tsv


title: Adult mouse brain cortex, rep 5, RNA-seq


title: Adult mouse brain cortex, rep 4, RNA-seq


title: E7.75_heart_cell8


title: Adult mouse brain cortex, rep 8, RNA-seq


title: HEK293T-HEKsite2-control-rep2

description:
245A
nCas9
processed data: ABE_SECURE_counts.tsv


title: HEK293T-HEKsite2-miniABEmax-rep1

description:
244C
miniABEmax
processed data: ABE_SECURE_counts.tsv


title: Adult mouse brain cortex, rep 3, RNA-seq


title: sir2

description: ribo-minus  RNA


title: E7.75_heart_cell6


title: BY4741

description: ribo-minus  RNA


title: E7.75_heart_cell7


title: E7.75_heart_cell10


title: E7.75_heart_cell5


title: Pleura 3

description:
Table_S3.xlsx
Table_S4.xlsx

organism:
Streptococcus pneumoniae
Mus musculus

source_name: Pleural Flluid

value: Neutrophils + bacteria

value: C57BL/6 + SRL1


title: Adult mouse brain cortex, rep 2, RNA-seq


title: Adult mouse brain cortex, rep 6, RNA-seq


title: Adult mouse brain cortex, rep 1, RNA-seq


title: fpr3

description: ribo-minus  RNA


title: Pleura 1

description:
Table_S3.xlsx
Table_S4.xlsx

source_name: Pleural Fluid


title: HEK293T-NT-miniABEmax-rep3

description:
251C
miniABEmax
processed data: ABE_SECURE_counts.tsv

value: NT guide:GGAGACGATTAATGCGTCTC


title: CLL-like-U0975-CD21

city: Columbus

first: Pearlly

last: Yan

state: OH

department: Division of Hematology

institute: The Ohio State University

description: spleen tissue obtained from diseased mouse meeting euthanasia criteria

data_processing:
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the mouse decontaminome using HISAT2 v2.0.6 using default parameters
Unaligned deconaminome reads were aligned against the mouse genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release M14
Genome_build: GRCm38p4
Supplementary_files_format_and_content: TSV Counts tables generated using Subread FeatureCounts, Unfiltered

source_name: spleen single cell suspension

growth_protocol: spleen suspension cells cryopreserved prior to sorting, surface staining directly after thawing and immediate flow sorting

extract_protocol:
RNA isolation was performed using a chloroform/ alcohol extraction method. Trizol preparations were brought to room temperature (RT). Volumes were adjusted to 1ml Trizol. After 1h at RT, 200µl chloroform and 1µl glycogen were added. Tubes were shaken vigorously by hand for 15 seconds, incubated at RT for 3 minutes at RT, and centrifuges at 12000g for 15 minutes at 4°C. The aqueous phase was transferred to a fresh 1.7ml tube, and 500µl 100% isopropanol were added. Tubes were vortexed, incubated at RT for 10 minutes, and centrifuged at 12000g for 15 minutes at 4°C. The pellet was washed with 500µl 75% ethanol, vortexed, and centrifuged at 750g for 5 minutes at 4°C. Supernatant was discarded completely, and the pellet was allowed to air dry for 5-10 minutes before resuspending in 20µl RNase/DNase free water. RNA concentrations and purities were assessed by nanodrop, and bioanalyzer.
Total RNA quantified using the Invitrogen Qubit RNA HS Assay kit (Invitrogen, Carlsbad, CA) was serially diluted to masses characteristic of single- and low cell number RNA-Seq (1ng). The Clontech SMARTer v4 kit (Takara Bio USA, Inc., Mountain View, CA) was used for global preamplification. Illumina sequencing library was derived from the resultant cDNA using the Illumina Nextera XT DNA Library Prep Kit (Cat. # 15031942).

treatment_protocol: sorted spleen cells collected in PBS 10%FBS on ice, washed 1x with PBS, resuspended in Trizol, stored at -80C until extraction

tag: input rna mass

value: 1 ng

tag: sorted cells

value: CD19+CD5+, gated on viable CD3-CD11b-CD93- spleen cells

tag: genotype/variation

value: Eu-TCL1xMyc strain

tag: mouse


title: HEK293T-HEKsite2-ABEmax-rep1

description:
244B
ABEmax
processed data: ABE_SECURE_counts.tsv

tag: cell line

tag: treatment

tag: guide rna

value: HEKsite2 guide:GAACACAAAGCATAGACTGC


title: E7.75_heart_cell2

tag: strain

tag: age

value: heart cell


title: HEK293T-NT-miniABEmax_variant2-rep3

description:
251E
miniABEmax(V82G)
processed data: ABE_SECURE_counts.tsv

tag: gfp


title: Lung 3

description:
Table_S3.xlsx
Table_S4.xlsx

source_name: BALF fluid

tag: cell type


title: E7.75_heart_cell3

tag: chip antibody


title: HEK293T-HEKsite2-control-rep1

description:
244A
nCas9
processed data: ABE_SECURE_counts.tsv


title: E7.75_heart_cell1


title: Lung 1

description:
Table_S3.xlsx
Table_S4.xlsx


title: Lung 2

description:
Table_S3.xlsx
Table_S4.xlsx


title: IgMplus-U0975-CD21

value: CD21-IgM+, gated on viable CD3-CD11b-CD5-CD93-CD19+ spleen cells


title: Pleura 2

description:
Table_S3.xlsx
Table_S4.xlsx


title: HEK293T-NT-miniABEmax_variant1-rep3

description:
251D
miniABEmax(K20A+R21A)
processed data: ABE_SECURE_counts.tsv


title: Mta2_VavKO_931t14

data_processing:
Basecalls performed using CASAVA version 1.82
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
RNA-seq reads were aligned to the mm9 genome assembly using STAR with default parameters
Transcript abundances were estimated reported as raw read counts using Rsubread
Differential expression was analyzed using R script
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes read counts for each sample

source_name: small pre-B cell

extract_protocol:
Small Pre-B cells were sorted by surface markers B220+IgM-CD43- and cell size indicated by FSC and SSC pattern and RNA was harvested using QIAGEN RNeasy Mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols with Illumina TruSeq Stranded mRNA Preparation Kit (Illumina)

tag: tissue

value: bone marrow

value: small pre-B cell


title: IgMneg-U0975-CD21

value: CD21-IgM-, gated on viable CD3-CD11b-CD5-CD93-CD19+ spleen cells


title: Mta2_VavKO_918t4


title: Control_931t10

value: Control


title: Control_919t7


title: Mta2_VavKO_919t6


title: Control_918t3


title: Mta2_VavKO_789t6

source_name: pro-B cell

extract_protocol:
Pro-B cells were sorted based on surface markers B220+IgM-CD43+ and RNA was harvested using QIAGEN RNeasy Mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols with Illumina TruSeq Stranded mRNA Preparation Kit (Illumina)

value: pro-B cell


title: HEK393T-NT-miniABEmax-rep2

description:
250C
miniABEmax
processed data: ABE_SECURE_counts.tsv

value: All GFP


title: HEK393T-NT-miniABEmax_variant2-rep2

description:
250E
miniABEmax(V82G)
processed data: ABE_SECURE_counts.tsv


title: HEK293T-NT-ABEmax-rep3

description:
251B
ABEmax
processed data: ABE_SECURE_counts.tsv


title: HEK293T-NT-control-rep3

description:
251A
nCas9
processed data: ABE_SECURE_counts.tsv


title: HEK393T-NT-miniABEmax_variant1-rep2

description:
250D
miniABEmax(K20A+R21A)
processed data: ABE_SECURE_counts.tsv


title: HEK293T-NT-miniABEmax_variant2-rep1

description:
243E
miniABEmax(V82G)
processed data: ABE_SECURE_counts.tsv


title: HEK293T-NT-miniABEmax_variant1-rep1

description:
243D
miniABEmax(K20A+R21A)
processed data: ABE_SECURE_counts.tsv


title: HEK393T-NT-ABEmax-rep2

description:
250B
ABEmax
processed data: ABE_SECURE_counts.tsv


title: HEK393T-NT-control-rep2

description:
250A
nCas9
processed data: ABE_SECURE_counts.tsv


title: IgMplus-C1445-CD21


title: IgMplus-C1451-CD21


title: IgMneg-C1445-CD21


title: IgMneg-C1451-CD21


title: CLL-like-C1445-CD21


title: BZ_120_2

city: Madison

first: Laura

last: Knoll

state: WI

address: 1550 Linden Drive

department: Medical Microbiology and Immunology

institute: UW-Madison

data_processing:
Base calling using standard Illumina HiSeq2500 software
The raw files were filtered for quality and adapters clipped using trimmomatic v0.39
The filtered reads were aligned to the Toxoplasma genome (ToxoDB release 38), using the Spliced Alignment to a Reference (STAR; v2.7.0d) program (files with "ToxoDB").
ToxoDB alignments were fed into StringTie (v1.3.6) using the ToxoDB ME49 genome as the reference genome, and minimun transcript coverage cutoff value of 150. The filtered reads were re-aglinged using this StringTie transcript file (files with"StringTie").
Relative gene expression levels were estimated using the RNA-seq by Expectation-Maximization (RSEM v1.2.28) program for both ToxoDB and StringTie alignment files.
Genome_build: Toxoplamsa gondii ME49, ToxoDB, release 38
Supplementary_files_format_and_content: Text files lists genes with respective transcript names giving their total counts along with normalized expression representaed as TPM and FPKM values.

organism: Toxoplasma gondii

source_name: bradyzoite

growth_protocol: ME49 tachyzoites were infected intraperitoneally into CBA/J mice.

extract_protocol:
Total RNA was isolated using phenol/chloroform extraction and isopropanol precipitation.
RNA was processed using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara), using 7 rounds of cDNA amplification, then indexed using Nextera XT Index Kit (Illumina).

treatment_protocol: Brain tissue was homogenized and T. gondii cysts were isolated using dextran separation. Bradyzoites were released from cysts by pepsin digestion and stored in trizol.

tag: days postinfection


title: BZ_90_2


title: BZ_28_3


title: BZ_90_1


title: BZ_28_1


title: CLL-like-C1451-CD21


title: E7.75_heart_cell4

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "-N 1".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad"
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bed files of non-duplicated reads.

extract_protocol:
Crosslinked cells were treated with 0.3% SDS at 62°C. Transposition was set up by incubation at 55°C for 30 min, followed by addition of stopping buffer. Soluble chromatin was used for following ChIP experiments.  DNA was eluted from beads, reverse crosslinked and treated with proteinase K. Finally, DNA was extracted by pheno-chloroform.
After PCR enrichment using NEBNext Q5 Ultra II master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.


title: HEK293T-NT-miniABEmax-rep1

description:
243C
miniABEmax
processed data: ABE_SECURE_counts.tsv


title: BZ_120_3


title: HEK293T-NT-ABEmax-rep1

description:
243B
ABEmax
processed data: ABE_SECURE_counts.tsv


title: H3K4me3_1M-sonication-input-ESC

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "-N 1".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by samtools (v 1.3.1) rmdup.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad"
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 1 bp by “--scaleFactor, --binSize 1” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bigwig files. Bigwig files of sonication-ChIP showed the enriched signal of H3K4me3 across the whole genome. They were positive controls, approving that itChIP-seq did a better job.

growth_protocol: Mouse embryonic stem cells were cultured in DMEM/F12 with 2i or 15% fetal bovine serum, and MEFs in DMEM medium with 10% fetal bovine serum.

extract_protocol:
Crosslinked cells were lysed and sonciated to 200-800 bp fragments. Soluble chromatin was used for ChIP experiments. DNA on beads were tagmented with Tn5 transposome following the Nextera protocol.
After PCR enrichment using NEBNext Q5 Ultra II master mix, products were purified and size selected by AMPure XP beads for 200-1000 bp.

value: cultured mESC

tag: fixed by

value: formaldehyde for 3 min

value: no (input)


title: HEK293T-NT-control-rep1

description:
243A
nCas9
processed data: ABE_SECURE_counts.tsv


title: H3K4me3_1M-sonication-ChIP-ESC_rep2


title: H3K4me3_1M-sonication-ChIP-ESC_rep1


title: Control_789t7


title: ATAC-50K-ESC_rep1

description: Transposase-accessible chromatin

data_processing:
Basecalls performed using CASAVA version 1.8.2.
ATAC-seq reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "-N 1".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by samtools (v 1.3.1) rmdup.
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 1 bp by “--scaleFactor, --binSize 1” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files were bigwig files. Bigwig files showed the signal of reads distribution, reflecting the enrichment of open chromatin regions got from ATAC-seq.

growth_protocol: Mouse embryonic stem cells were cultured in DMEM/F12 with 2i or 15% fetal bovine serum.

extract_protocol:
Native cells were collected for 50,000 each group. Cells were lysed gently and tagmented by Tn5-MEA/B. After tagmentation, adaptor-ligated DNA was immediately extracted using QIAGEN QIAquick kit.
DNA was amplified for 14 cycles with NEBNext Q5 Ultra II master mix. The desirable size range was 200-800 bp, size-selected using AMPure XP beads. The sequencing strategy was on HiSeq 4000, for paired end 150 bp.

value: cultured native mouse embryonic stem cell (mESC)


title: Control_781t4


title: ATAC-50K-ESC_rep2

description: Transposase-accessible chromatin


title: Pooled normal rabbit IgG (Mock)ChIP'd DNA

status: Public on Jul 10 2019

city: Pittsburgh

first: Jian Ming

last: Khor

state: PA

address: 4400 Fifth Ave

department: Biological Sciences

institute: Carnegie Mellon University

description: Mock

data_processing:
Raw reads cleaned and trimmed using Filterbytile and Trimmomatic
Alignment to S. purpuratus genome using Bowtie2
Alignment quality control using Samtools
Peak calling using MACS2
Genome_build: S. purpuratus genome version 3.1 (available on http://www.echinobase.org)
Supplementary_files_format_and_content: Narrowpeak and BED files generated by MACS2 with an mfold of [5, 50] and a p-value cutoff of 0.005

organism: Strongylocentrotus purpuratus

source_name: Sea urchin embryos

extract_protocol:
Lysates were clarified from sonicated nuclei and Sp-Alx1-DNA complexes were isolated with antibody.
Library was prepared and sequenced by Novogene Corporation (Chula Vista, CA, USA) using Illumina-based sequencing (Illumina HiSeq 2500 SE50).

tag: developmental stage

value: Mesenchyme blastula stage embryos

value: Normal rabbit IgG (Sigma-Aldrich, Cat. No. 12370)


title: Pooled Sp-Alx1 ChIP'd DNA

value: Custom Sp-Alx1 antibody


title: Mta2_VavKO_781t3


title: H3K36me3 ChIP-seq of D248

first: Faming

address: 320 Yue Yang Road

department: CAS-MPG Partner Institute for Computational Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Read quality was checked using FastQC.
Raw sequencing reads were trimmed by quality using Trimmomatic.
Cleaned reads were mapped to the Os-Nipponbare-Reference-IRGSP-1.0 using BWA 0.7.12-r1039.
The returned alignments (BAM files) were stringently filtered by samtools so as to remove duplicates, ambiguously mapped reads and read pairs with conflicting alignments.
The reads per bin of filtered BAM files were normalized using deepTools.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: bigwig format files were generated and reads per bin were normalized using counts per million (CPM).

organism: Oryza sativa

source_name: leaf blades of 40 d seedling of early-maturing NIL D248

extract_protocol:
Fresh leaf blades of 40 d seedlings of early-maturing NIL D248 (BC5F11) and its recurrent parent SH881 (Shuhui881) were harvested for fixation. Chromatin was isolated and sonicated to generate DNA fragment with an average size of about 500 bp. The solubilized chromatin was immunoprecipitated by Protein A beads (Millipore) with anti-H3K36me3 antibody (Abcam, ab9050), and the co-immunoprecipitated DNA was recovered and analyzed by ChIP-seq.
More than 10 ng ChIP DNA each sample was used for Illumina library generation following the manufacturer’s instructions.

tag: rice line

value: Early-maturing NIL D248

value: 40 d seedling

value: Leaf blades


title: H3K36me3 ChIP-seq of SH881

source_name: leaf blades of 40 d seedling of recurrent parent SH881

value: Recurrent parent SH881


title: exosome_rmTBI_14d_rep3

city: Tianjin

first: Xintong

last: Ge

address: 154, Anshan Road

department: Department of Neurosurgery

institute: Tianjin Medical University General Hospital

description: miRNA expression in microglial exosomes of rmTBI mice at 14 days post-injury, replicate 3

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: microglial exosome, rmTBI 14d post-injury, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The mice were subjected to closed-head injury after anesthesia with 4.6% isoflurane. A molded acrylic cast was designed to fix the mice and provide their heads with a 3.0-mm space below for acceleration and deceleration beneath the point of impact. The mouse was secured in prone position on the acrylic cast with surgical tape across the shoulders, which was installed on the stereotaxic device. After shaving the head, a self-designed standard manufacturing concave metal disc was adhered to the skull immediately caudal to bregma as a helmet, in order to transmit the hitting power to the whole brain. Specifically, scalp incision was not performed to better stimulate the injured procedure of rmTBI patients. The impounder tip of the injury device (electronic CCI model 6.3, American Instruments, Richmond, VA, USA) was then extended to its full impact distance, positioned on the center of the disc surface, and reset to induce an impact. It was discharged at 5.0 m/s with a head displacement of 2.5 mm. After the impact, the mice were placed in a well-ventilated cage at 37 ℃ until they regained consciousness. Repetitive injury was induced for totally 4 times with a 48-h interval. Sham-operated mice underwent the same procedures except for the impact.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: The mice were sacrificed at 1, 3, 7, 14, 21, 28, 35 and 42 DPI by transcardiac perfusion with PBS. The brain were dissected on the ice, and incubated the isolated injured hemisphere with 3-ml Hibernate-A cell culture medium (ThermoFisher Scientific, Waltham, MA, USA). The samples were digested by 20 units/ml of papain (Solarbio, Beijing, China) for 15 min at 37 ℃, and were stopped by adding 6-ml Hibernate-A cell culture medium (pre-stored at 4 ℃). After that, repeated blowing was performed using a dropper to remove the brain tissues. The samples were then centrifuged at 2000 × g for 10 min at 4 ℃, followed by spun at 10,000 × g for 30 min at 4 ℃ to further remove the cell debris. The supernatants were collected and filtered through a 0.22-μm filter gauze (MilliporeSigma, Billerica, MA, USA) to sieve out dead cells and large particles. Total Exosome Isolation Reagent (ThermoFisher Scientific) was then added to the supernatants at the proportion of 1-ml supernatants to 500-μl reagent. The samples were mixed by vortexing and incubated overnight at 4 ℃. On the next day, ultracentrifugation was performed at 100,000 × g for 70 min at 4 ℃. The supernatants were removed, and the pellets were collected and resuspended in 0.35-μL calcium- and magnesium-free Dulbecco’s PBS (ThermoFisher Scientific). For isolation of microglial exosomes, the samples were incubated with 1.5-μg rat anti-mouse CD11b bitinylated antibody (ThermoFisher Scientific) in 50-μL 3% BSA for 60 min at room temperature with mixing. They were then incubated with 10-μl Streptavidin-Plus UltraLink resin (ThermoFisher Scientific) in 40-μl 3% BSA for 30 min at room temperature. Finally, the samples were centrifuged at 800 × g for 10 min at 4 ℃.

value: cerebrum

tag: Sex

value: male


title: exosome_rmTBI_14d_rep2

description: miRNA expression in microglial exosomes of rmTBI mice at 14 days post-injury, replicate 2

source_name: microglial exosome, rmTBI 14d post-injury, replicate 2


title: exosome_rmTBI_42d_rep1

description: miRNA expression in microglial exosomes of rmTBI mice at 42 days post-injury, replicate 1

source_name: microglial exosome, rmTBI 42d post-injury, replicate 1


title: exosome_rmTBI_42d_rep2

description: miRNA expression in microglial exosomes of rmTBI mice at 42 days post-injury, replicate 2

source_name: microglial exosome, rmTBI 42d post-injury, replicate 2


title: EAT_2-week-old lamb_Maternal cortisol 0.5mg/kg/day_Replicate 9

city: Gainesville

first: Elaine

middle: Mary

last: Richards

state: FL

department: Pharmacodynamics

institute: University of Florida

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >13.7 pmol Cy3/µg cRNA) was fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) design 019921 by the ICBR facility at the University of Florida according to Agilent's methodology.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color (green) scan setting for 8x15k array slides, by the ICBR facility at University of Florida.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112)  background detrended Processed Signal. The limma package was employed to import the raw data into R (http://www.r-project.org), perform background correction and normalize the data by the quantile normalization method. Control probes and low expressed probes were filtered out, retaining for further analysis the probes that were at least 10% brighter than the negative controls on at least six arrays.

organism: Ovis aries

source_name: Epicardial adipose tissue, 2-week-old lamb, maternal cortisol 0.5 mg/kg/day, gestational day 115 to term

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent, Newcastle DE) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted from epicardial adipose tissue with Trizol (Life Technologies, Carlsbad, CA), and purified through Qiagen RNeasy+ kits with on-column DNase digestion (QIAGEN, Valencia, CA) according to manufacturers' protocols.Total RNA concentration was measured by Nanodrop ND-1000 and RNA quality was monitored by Agilent Bioanalyzer.

treatment_protocol: Ewes were treated with no or 1mg/kg/day cortisol (term fetuses) or 0.5mg/kg/day cortisol (2-week-old lambs). Fetuses and lambs were not treated; their cortisol increased secondary to maternal treatment. Lambs and term fetuses were exposed to different levels of increased maternal cortisol so direct comparisons of these two groups of increased maternal cortisol could not be made.

value: Epicardial adipose tissue

value: Two-week-old lamb


title: EAT_2-week-old lamb_Maternal cortisol 0.5mg/kg/day_Replicate 5


title: exosome_control_rep1

description: miRNA expression in microglial exosomes of sham mice brain, replicate 1

source_name: microglial exosome, control, replicate 1


title: exosome_rmTBI_3d_rep1

description: miRNA expression in microglial exosomes of rmTBI mice at 3 days post-injury, replicate 1

source_name: microglial exosome, rmTBI 3d post-injury, replicate 1


title: exosome_rmTBI_42d_rep3

description: miRNA expression in microglial exosomes of rmTBI mice at 42 days post-injury, replicate 3

source_name: microglial exosome, rmTBI 42d post-injury, replicate 3


title: exosome_rmTBI_3d_rep2

description: miRNA expression in microglial exosomes of rmTBI mice at 3 days post-injury, replicate 2

source_name: microglial exosome, rmTBI 3d post-injury, replicate 2


title: EAT_2-week-old lamb_Maternal cortisol 0.5mg/kg/day_Replicate 7


title: exosome_rmTBI_3d_rep3

description: miRNA expression in microglial exosomes of rmTBI mice at 3 days post-injury, replicate 3

source_name: microglial exosome, rmTBI 3d post-injury, replicate 3


title: exosome_control_rep3

description: miRNA expression in microglial exosomes of sham mice brain, replicate 3

source_name: microglial exosome, control, replicate 3


title: exosome_control_rep2

description: miRNA expression in microglial exosomes of sham mice brain, replicate 2

source_name: microglial exosome, control, replicate 2


title: EAT_2-week-old lamb_Maternal cortisol 0.5mg/kg/day_Replicate 6


title: exosome_rmTBI_14d_rep1

description: miRNA expression in microglial exosomes of rmTBI mice at 14 days post-injury, replicate 1

source_name: microglial exosome, rmTBI 14d post-injury, replicate 1


title: EAT_2-week-old lamb_Maternal cortisol 0.5mg/kg/day_Replicate 4


title: EAT_2-week-old lamb_Untreated_Replicate 6

source_name: Epicardial adipose tissue, 2-week-old lamb, untreated


title: EAT_2-week-old lamb_Maternal cortisol 0.5mg/kg/day_Replicate 3


title: EAT_2-week-old lamb_Untreated_Replicate 7


title: EAT_2-week-old lamb_Untreated_Replicate 3


title: EAT_2-week-old lamb_Maternal cortisol 0.5mg/kg/day_Replicate 1


title: EAT_Term Fetus_Maternal cortisol 1mg/kg/day_Replicate 6

source_name: Epicardial adipose tissue, term fetus, maternal cortisol 1mg/kg/day, gestational day 115 to term

value: Term fetus


title: SETD5+/-_T20_rep3

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

data_processing:
Reads from three independent sequenced libraries for each cell type and experimental time point were merged and their quality was assessed by using fastQC (https://www.bioinformatics.babraham.ac.uk  /projects/fastqc/).
Total reads were aligned to the mouse genome (GRCm38/mm10) using TopHat v2.1.1 (https://ccb.jhu.edu/software/tophat/index.shtml) and discarding ambiguous reads mapping at multiple sites. The average mappability was higher than 96% of initial total reads. Duplicated reads were discarded for further analysis.
Normalized BigWig tracks of chrom-RNA-seq signals were generated with bedtools 2.24.0 (http://bedtools.readthedocs.io/en/latest/) and the bedGraphToBigWig program (https://www.encodeproject.org/software/bedgraphtobigwig/) and visualized in the UCSC Genome Browser (http://genome.ucsc.edu/).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: The bigwig files of merged mapped reads from 3 independent biological replicates

source_name: neural stem cells

growth_protocol: NSCs were routinely cultured in suspension as neurospheres. Cells were cultured in neural inducing medium (NIM) composed of: DMEM/F12 (Sigma-Aldrich) supplemented with Hormon Mix (DMEM/F12, 0,6% Glucose (Sigma-Aldrich) (30%in phosphate buffer (PBS) (Euroclone)), Insulin (Sigma-Aldrich) 250μg/ml, putrescin powder (Sigma-Aldrich) 97μg/ml, apotransferrin powder (Sigma Aldrich), sodium selenite 0,3μM, progesterone 0,2μM), 1mg/ml penicillin/streptomycin (Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich), 0,66% Glucose (30% in phosphate buffer salt (PBS) (Euroclone)), Heparin 4μg/ml, 10 ng/ml bFGF (basic fibroblast growth factor) (ThermoFisher Scientific) and 10 ng/ml EGF (epithelial growth factor) (ThermoFisher Scientific).

extract_protocol:
Cells were lysed in HLB/NP40 buffer (10 mM Tris-Hcl, pH 7.5, 10 mM NaCl, 0.5% NP40, and 2.5 mM MgCl2) 5 minutes in ice. Nuclei were isolated by under-laying HLB/NP40/Sucrose buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% NP40, 2.5 mM MgCl2, and 10% Sucrose) and centrifuging at 1400 g for 5 minutes at 4°C. The chromatin fraction was isolated by resuspending the nuclei in 125 μl of NUN1 solution (20 mM Tri-HCl, pH 8.0, 75 mM NaCl, 0.5 mM EDTA, 50% Glycerol and proteinase inhibitor) followed by 1.2 ml NUN2 buffer (20 mM HEPES-KOH pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% NP40, proteinase and phosphatase inhibitor cocktail), incubating on ice for 15 minutes and centrifuging at 15000 g for 10 minutes at 4°C. Chromatin-bound RNA was extracted with Trizol reagent (Thermo Fisher cat. #15596026). DNA and ribosomal RNA contaminants were removed by DNase (Qiagen cat. #79254) and RiboZero (Illumina cat. # MRZG12324) treatments, respectively. RNA quality and concentration were assed at the 2100 Bioanalyzer (Agilent cat. #G2939BA) and the Qubit fluorometer (Thermo Fisher cat. # Q33226), respectively.
Chrom-RNA-seq libraries were prepared by using the stranded Small RNA Library Prep Kit (Illumina cat. # RS-200-0012), with minor modifications and sequenced as single reads of 50 bp with the Illumina HiSeq2500. Three independent biological replicates were performed for each cell line and time point and sequenced as independent libraries.

treatment_protocol: Cells were plated in adherent condition using Matrigel coated 15mm plates at a density of 6x10^6 per plate. When the plates reached 80% of confluence, cells were treated with 100 µM 5,6-dichlorobenzimidazole 1-β-d-ribofuranoside (DRB, Sigma cat. #D1916) for 3 hours in culture medium. Inhibition of transcription elongation was released by washing the cells twice with PBS and incubating them with fresh complete medium for transcription restart. After 5, 10 and 20 minutes of transcription release, cells were washed twice in PBS and collected. A control for DRB inhibition without transcription release was also performed.

value: NSCs were derived from telencephalic cortex of embryos at E14.5

tag: time point (min)

value: DRB-treated cells+DRB release after 20'


title: EAT_2-week-old lamb_Untreated_Replicate 2


title: EAT_2-week-old lamb_Maternal cortisol 0.5mg/kg/day_Replicate 8


title: SETD5+/-_T20_rep2

tag: genotype/variation


title: EAT_2-week-old lamb_Untreated_Replicate 1


title: SETD5+/-_T20_rep1


title: EAT_Term Fetus_Maternal cortisol 1mg/kg/day_Replicate 4


title: EAT_Term Fetus_Untreated_Replicate 5

source_name: Epicardial adipose tissue, term fetus, untreated


title: EAT_Term Fetus_Maternal cortisol 1mg/kg/day_Replicate 3


title: SETD5+/-_T10_rep3

value: DRB-treated cells+DRB release after 10'


title: EAT_Term Fetus_Untreated_Replicate 6


title: EAT_2-week-old lamb_Untreated_Replicate 5


title: EAT_Term Fetus_Maternal cortisol 1mg/kg/day_Replicate 5


title: EAT_Term Fetus_Untreated_Replicate 7


title: EAT_2-week-old lamb_Maternal cortisol 0.5mg/kg/day_Replicate 2


title: EAT_Term Fetus_Untreated_Replicate 8


title: EAT_Term Fetus_Untreated_Replicate 3


title: EAT_Term Fetus_Untreated_Replicate 2


title: SETD5+/-_T5_rep3

value: DRB-treated cells+DRB release after 5'


title: EAT_Term Fetus_Maternal cortisol 1mg/kg/day_Replicate 1


title: EAT_Term Fetus_Untreated_Replicate 1


title: SETD5+/-_T5_rep2


title: SETD5+/-_T0_rep2

value: DRB-treated cells


title: SETD5+/-_T5_rep1


title: SETD5+/-_T0_rep3


title: WT_T20_rep3

value: wild type


title: SETD5+/-_T0_rep1


title: WT_T20_rep1


title: SETD5+/-_T10_rep2


title: WT_T10_rep1


title: WT_T10_rep2


title: WT_T5_rep2


title: EAT_2-week-old lamb_Untreated_Replicate 4


title: WT_T0_rep1


title: WT_T0_rep3


title: SETD5+/-_T10_rep1


title: WT_T0_rep2


title: EAT_Term Fetus_Untreated_Replicate 4


title: Y3_AE: RNAseq_OLD_AE_2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description: protocol name: RNA-Seq_small_intestine_sorted_cells

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse GRCm38 genome assembly using HISAT2 2.1.0 (no soft clipping). BAM files were imported to Seqmonk v1.43.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: RNA-Seq DEseq2 report: Quantitated differential expression data files are tab delimited and contains the following columns: (1) probe name; (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-17) log2 RPM value - opposing strand specific quantitation by sample; (18-19) DESeq2 FDR -log(10) transformed if significant (P<0.05, multiple testing corrected) in ISC or AE.
Supplementary_files_format_and_content: RNA-Seq raw count report: Raw read count quantitation file is tab delimited and contains the following columns: (1) probe name; (2) Chromosome; (3) Start; (4) End; (5) Strand; (6-17) raw read count quantitation, opposing strand specific quantitation by sample

source_name: small intestine villus

extract_protocol:
Villus cell suspensions for RNA-seq were stained in 2% fetal calf serum/PBS with 1:200 APC-conjugated Epcam antibodies (CD326, eBioscience 17-5791-82), 1:1000 AF488-conjugated CD45 antibodies (Biolegend 103122) and 1:1000 AF488-conjugated CD31 antibodies (Biolegend 102414) for 15 minutes at room temperature, washed 3 times and resuspended in 2% FCS/PBS with 3.2µg/ml ROCK-inhibitor (Y-27632, Sigma). Epcamhigh CD31- CD45- DAPI- cells were sorted on BD Aria III SORP cell sorter with 100 µM nozzle. ISC (GFPhigh DAPI-) for RNA-seq were isolated from crypt suspensions of Lgr5-GFP+ mice and processed as above except the staining step. 60-100 thousand cells were sorted into RLT buffer for subsequent RNA-isolation according to manufacturer’s protocol with the Qiagen RNeasy Micro kit with on-column DNA digestion. Quantity and quality were measured with an Agilent Bioanalyzer Eukaryote Total RNA Pico assay.
Libraries were generated from 35 ng total RNA according to NEB Ultra II Directional RNA Library Preparation Kit for Illumina (E7760), Poly(A) mRNA magnetic isolation module (E7490) and multiplex oligos (E7335) manuals with the following modifications: 14 PCR-amplification cycles were performed. SPRI select beads were substituted with Seramag Speedbeads (Thermo scientific 65152105050250) for size selection steps.

value: adult enterocytes

value: small intestine villus

value: C57BL/6 Lgr5-GFP


title: Y3_ISC: RNAseq_OLD_AE_3


title: WT_T5_rep3


title: WT_T10_rep3


title: Y2_AE: RNAseq_YOUNG_AE_3


title: Y1_ISC: RNAseq_YOUNG_AE_2


title: Y1_AE: RNAseq_YOUNG_AE_1


title: O5_ISC: RNAseq_OLD_ISC_3

source_name: small intestine crypt

value: stem cells

value: small intestine crypt


title: Y2_ISC: RNAseq_OLD_AE_1


title: WT_T20_rep2


title: EAT_Term Fetus_Maternal cortisol 1mg/kg/day_Replicate 2


title: O3_AE: RNAseq_YOUNG_ISC_3


title: O3_ISC: RNAseq_OLD_ISC_1


title: O1_ISC: RNAseq_YOUNG_ISC_2


title: O1_AE: RNAseq_YOUNG_ISC_1


title: WT_T5_rep1


title: O5_AE: RNAseq_OLD_ISC_2


title: Blood_TD_Rep20

city: Sacramento

first: Boryana

last: Stamova

address: 2805 50th Street

department: Neurology; MIND Institute

institute: University of California, Davis Medical Center

hyb_protocol: Hybridization, washing and laser scanning of Affymetrix Human Exon 1.0 ST microarrays were performed according to protocol (Affymetrix, Santa Clara, CA).

data_processing: Raw CEL file data was uploaded in Partek Genomics Suite and was RMA-normalized.

source_name: typically developing (TD) control

label_protocol: 20 ng RNA samples were amplified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) with the exon Module. The samples were fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

growth_protocol: Not applicatble

extract_protocol: Whole blood  was collected from each subject via antecubital fossa venipuncture into PAXgene Vacutainer tubes (Qiagen, Valencia, CA, USA). These tubes contain a solution that immediately lyses all of the cells in whole blood and stabilizes the RNA without measurable degradation. Blood was collected in PaxGen tubes. WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) with the Exon Module and fragmented and labeled using the FL Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

treatment_protocol: Not applicatble

tag: gender

value: blood


title: Blood_TD_Rep19

scan_protocol: Hybridization, washing and laser scanning of Affymetrix Human Exon 1.0 ST microarrays were performed according to protocol (Affymetrix, Santa Clara, CA).


title: Blood_TD_Rep18


title: Blood_TD_Rep9


title: Blood_TD_Rep10


title: Blood_TD_Rep15


title: Blood_TD_Rep16


title: Blood_ASD_Rep24

source_name: Ausitm Spectrum Disorders, Normal Total Cerebral Volume (ASD_NTCV)


title: Blood_TD_Rep17


title: Blood_TD_Rep4


title: Blood_TD_Rep14


title: Blood_TD_Rep6


title: Blood_ASD_Rep21


title: Blood_ASD_Rep27


title: Blood_TD_Rep1


title: Blood_TD_Rep2


title: Blood_ASD_Rep23


title: Blood_ASD_Rep22


title: Blood_TD_Rep12


title: Blood_TD_Rep11


title: Blood_TD_Rep5


title: Blood_TD_Rep8


title: Blood_ASD_Rep25


title: Blood_TD_Rep3


title: Blood_TD_Rep13


title: Blood_ASD_Rep26


title: Blood_ASD_Rep29


title: Blood_TD_Rep7


title: Blood_ASD_Rep19


title: Blood_ASD_Rep30


title: Blood_ASD_Rep18


title: Blood_ASD_Rep28


title: Blood_ASD_Rep20


title: Blood_ASD_Rep13


title: Blood_ASD_Rep17


title: Blood_ASD_Rep14


title: Blood_ASD_Rep15


title: Blood_ASD_Rep12


title: Blood_ASD_Rep7

source_name: Ausitm Spectrum Disorders, Large Total Cerebral Volume (ASD_LTCV)


title: Blood_ASD_Rep4


title: Blood_ASD_Rep9


title: Blood_ASD_Rep5


title: Patient 11 HCV+ Whole liver tissue

first: Erin

middle: Heather

last: Doyle

address: 1425 Madison Ave

department: Liver

institute: Icahn School of Medicine at Mount Sinai

description:
Biological replicate 3
mHCV_11

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio software

source_name: Human Liver Tissue

label_protocol: Illumina protocol

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Bioanalyser.

tag: patients

value: Liver


title: Patient 12 HCV+ Whole liver tissue

description:
Biological replicate 4
mHCV_12


title: Patient 15 HCV+ Whole liver tissue

description:
Biological replicate 6
mHCV_15


title: Patient 14 HCV+ Whole liver tissue

description:
Biological replicate 5
mHCV_14


title: Patient 17 HCV+ Whole liver tissue

description:
Biological replicate 8
mHCV_17


title: Patient 19 HCV+ Whole liver tissue

description:
Biological replicate 10
mHCV_19


title: Patient 3 HCV+ Whole liver tissue

description:
Biological replicate 1
mHCV_3


title: Blood_ASD_Rep2

value: male


title: Blood_ASD_Rep8


title: Blood_ASD_Rep11


title: Blood_ASD_Rep6


title: Patient 20 HCV+ Whole liver tissue

description:
Biological replicate 11
mHCV_20


title: Patient 20/4 LMCs R848

description:
Biological replicate 6
A20-4LR

source_name: Human LMCs

tag: stimulation


title: Blood_ASD_Rep1


title: Blood_ASD_Rep3


title: Patient 20/4 LMCs LPS

description:
Biological replicate 6
A20-4LL

value: LPS


title: Patient 10 HCV+ Whole liver tissue

description:
Biological replicate 2
mHCV_10


title: Patient 20/4 LMCs media

description:
Biological replicate 6
A20-4LM

value: Media


title: Blood_ASD_Rep10


title: Patient 20/4 PBMCs R848

description:
Biological replicate 6
A20-4PR

source_name: Human PBMCs

value: Blood


title: Patient 20/4 LMCs ex vivo

description:
Biological replicate 6
A20-4LE

value: Ex vivo


title: Patient 20/4 PBMCs media

description:
Biological replicate 6
A20-4PM


title: Patient 20/4 PBMCs ex vivo

description:
Biological replicate 6
A20-4PE


title: Patient 19/8 LMCs media

description:
Biological replicate 5
A19-8LM


title: Patient 19/8 LMCs R848

description:
Biological replicate 5
A19-8LR


title: Blood_ASD_Rep16


title: Patient 19/8 PBMCs ex vivo

description:
Biological replicate 5
A19-8PE


title: Patient 19/8 LMCs Poly I:C

description:
Biological replicate 5
A19-8LP

value: Poly I:C


title: Patient 19/8 PBMCs LPS

description:
Biological replicate 5
A19-8PL


title: Patient 20/4 PBMCs LPS

description:
Biological replicate 6
A20-4PL


title: Patient 19/8 PBMCs Poly I:C

description:
Biological replicate 5
A19-8PP


title: Patient 16/15 PBMCs LPS

description:
Biological replicate 4
A16-15PL


title: Patient 16/15 PBMCs Poly I:C

description:
Biological replicate 4
A16-15PP


title: Patient 16/15 LMCs Poly I:C

description:
Biological replicate 4
A16-15LP


title: Patient 19/8 PBMCs R848

description:
Biological replicate 5
A19-8PR


title: Patient 16/15 PBMCs R848

description:
Biological replicate 4
A16-15PR


title: Patient 19/8 LMCs ex vivo

description:
Biological replicate 5
A19-8LE


title: Patient 19/8 PBMCs media

description:
Biological replicate 5
A19-8PM


title: Patient 16/15 LMCs media

description:
Biological replicate 4
A16-15LM


title: Patient 16/15 PBMCs media

description:
Biological replicate 4
A16-15PM


title: Patient 16/15 LMCs LPS

description:
Biological replicate 4
A16-15LL


title: Patient 16/15 PBMCs ex vivo

description:
Biological replicate 4
A16-15PE


title: Patient 16/15 LMCs ex vivo

description:
Biological replicate 4
A16-15LE


title: Patient 14/17 LMCs Poly I:C

description:
Biological replicate 3
A14-17LP


title: Patient 14/17 LMCs ex vivo

description:
Biological replicate 3
A14-17LE


title: Patient 14/17 LMCs LPS

description:
Biological replicate 3
A14-17LL


title: Patient 14/17 LMCs media

description:
Biological replicate 3
A14-17LM


title: Patient 14/17 PBMCs R848

description:
Biological replicate 3
A14-17PR


title: Patient 14/17 PBMCs LPS

description:
Biological replicate 3
A14-17PL


title: Patient 12/13 LMCs R848

description:
Biological replicate 2
A12-13LR


title: Patient 12/13 LMCs media

description:
Biological replicate 2
A12-13LM


title: Patient 14/17 PBMCs media

description:
Biological replicate 3
A14-17PM


title: Patient 12/13 LMCs LPS

description:
Biological replicate 2
A12-13LL


title: Patient 12/13 LMCs Poly I:C

description:
Biological replicate 2
A12-13LP


title: Patient 14/17 PBMCs ex vivo

description:
Biological replicate 3
A14-17PE


title: Patient 12/13 PBMCs LPS

description:
Biological replicate 2
A12-13PL


title: Patient 12/13 PBMCs Poly I:C

description:
Biological replicate 2
A12-13PP


title: Patient 12/13 LMCs ex vivo

description:
Biological replicate 2
A12-13LE


title: Patient 14/17 PBMCs Poly I:C

description:
Biological replicate 3
A14-17PP


title: Patient 12/13 PBMCs R848

description:
Biological replicate 2
A12-13PR


title: Patient 11/3 LMCs ex vivo

description:
Biological replicate 1
A11-3LE


title: Patient 11/3 PBMCs R848

description:
Biological replicate 1
A11-3PR


title: Patient 11/3 LMCs media

description:
Biological replicate 1
A11-3LM


title: Patient 11/3 LMCs Poly I:C

description:
Biological replicate 1
A11-3LP


title: Patient 11/3 PBMCs Poly I:C

description:
Biological replicate 1
A11-3PP


title: Patient 12/13 PBMCs media

description:
Biological replicate 2
A12-13PM


title: Patient 11/3 PBMCs LPS

description:
Biological replicate 1
A11-3PL