title: phyAB-RL rep1

first: weiwei

last: Qi

address: No 99 Shangda Road

institute: Shanghai  University

description: replicate 1

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR 10 whole genome using bowtie0.12.5  with parameters default
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al,Nature methods 2008.
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: seedlings

growth_protocol: seeds were germinated in 1/2 MS plus 1% sucrose and placed at 4 degree centigrade for 3 days and then tranferred to white light for 12 h before placed in darkness  for  5 days, or  kept in darkness  for  5 days then exposed  to 50 μmol m-2 s-1 red light for 1hr.

extract_protocol:
RNA was extracted with RNAprep plant kit from TIANGEN, followed by DNase I (Takara) treatment. Quality control was performed with Agilent Bioanalyser. mRNA was purifed with Dynabeads® Oligo (dT)25（Life).  RNA libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: seedlings were kept in darkness  for  5 days, or  kept in darkness  for  5 days then exposed  to 50 μmol m-2 s-1 red light for 1hr.

value: phyAB

tag: light condition

value: 50 μmol/m6/s red light

tag: growth time

value: 5 days


title: DNAm_Subject_2101181

status: Public on Mar 01 2021

type: genomic

city: Chapel Hill

first: Julia

last: Rager

state: NC

address: 135 Dauer Drive, CB 7431

country: USA

institute: UNC

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
Raw idat files were loaded into R using the R package minfi
Samples were evaluated for potential sex mismatch, and probes were removed if they had detection p-values < .1 in more than 10% of samples
Raw data were normalized using functional normalization and normal-exponential out-of-band background correction using the R package minfi
Normalized data were corrected for batch effects using ComBat from the R package sva
Beta values are provided as a .csv, post normalization and QC

molecule: genomic DNA

organism: Homo sapiens

source_name: Placenta of infants born at low gestational age

label_protocol: Extracted DNA was bisulphate-converted using the EZ DNA methylation kit (Zymo Research, Irvine, CA), followed by quantification using the Infinium MethylationEPIC BeadChip (Illumina, San Diego, CA).

extract_protocol: Recruited patients from the ELGAN cohort that were scheduled to give birth at participating institutions between 2002 to 2004. Patients involved in the study comprised of pregnancies that ended in livebirths prior to completing 28 weeks of gestation.  Maternal, demographic, and clinical assessments were taken before and after delivery. Each infant's anthropometric measures were recorded throughout hospitalization and at follow-up. Placenta samples were collected immediately after surgery and stored at -80 degrees C until further analysis.  DNA molecules with 18 nucleotides or greater were extraced with the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). and extracted DNA was bisulphate-converted using the EZ DNA methylation kit (Zymo Research, Irvine, CA), followed by quantification using the Infinium MethylationEPIC BeadChip (Illumina, San Diego, CA)

tag: tissue

value: placenta

tag: birthweight (grams)

tag: infant sex

value: Female

tag: mage (age of mother) (years)

tag: bmi (body mass index)


title: DNAm_Subject_2101161

value: Male


title: DNAm_Subject_2101182


title: SA04785_S16

type: SRA

city: Los Angeles

first: Yu-Ling

last: Chang

state: California

address: 10833 Le Conte Ave

department: Pathology and Laboratory Medicine

institute: University of California, Los Angeles

library_source: genomic

data_processing:
Read quality was checked using FastQC (version 0.11.7)
Reads with the adaptors and the terminal CG were trimmed using the trimmomatic software (v0.38)
Reads aligned using BS-Seeker2 pipeline with the aligner bowtie (v1.2.2)
Genome_build: cohort1(Hg19); cohort2(Hg38)
Supplementary_files_format_and_content: [CGfinal files] chromosome, dinucleotide, position, methylated counts, total counts, methylation frequency, 95% confidence interval for methylation frequency;  [CGmap] Columns are: 1. chromosome, 2. nucleotide on Watson (+) strand, 3. position, 4. context (CG/CHG/CHH), 5. dinucleotide context (CA/CC/CG/CT), 6. methylation-level = #_of_C/ (#_of_C + #_of_T), 7. #_of_C (methylated C, the count of reads showing C here), 8. #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here).

source_name: Peripheral blood

extract_protocol:
Genomic DNA was extracted from whole blood samples using QIAGEN’s QIAamp DNA Blood Midi/Maxi Kit, performed at Duke. The purified genomic DNA was shipped on ice to University of California, Los Angeles (UCLA) for RRBS library preparation. Genomic DNA was first quantified by Qubit dsDNA BR Assay Kit (ThermoFisher cat. Q32850). The RRBS libraries were prepared as described(52) with the following conditions. For each sample, 100 ng of purified genomic DNA was digested with 20 U of MspI (NEB, cat # R0106L) at 37°C o/n in the presence of RNase Cocktail Mix (Ambion, cat # AM2286). End-repair and adenylation tailing were performed by the addition of Klenow Fragment 3ʹ->5ʹ exo- (NEB, cat # M0212L) in the presence of dATP, dGTP, and d5meCTP (Fermentas). Adapter Ligation was performed by the addition of 0.3 µl of Illumina TruSeq methylated Adapters (Illumina, TruSeq Nano cat# FC-121-4001) and 1 µl of Quick T4 DNA Ligase (NEB cat# M2200L). Samples were pooled and purified using an equal volume of SPRI beads (Beckman Coulter, cat # B23318). Size-selection was performed using SPRI beads to enrich for fragments from 200 to 400 bp. Bisulfite treatment was performed using EpiTect Bisulfite kit (QIAGEN, cat # 59104) according to manufacturer’s protocol, except that two consecutive rounds of conversion were performed, for a total of 10 hr of incubation. Purified converted DNA was PCR amplified using MyTaq HS Mix (Bioline, cat# BIO-25045) and TruSeq PCR Primer Cocktail (Illumina, TruSeq Nano cat# FC-121-4001) according to the following protocol: initial denaturation at 98°C for 30 s; 12 cycles of 98°C for 15 s, 60°C for 30 s, 72°C for 30 s; final extension at 72°C for 5 min. Amplified libraries were purified twice with an equal amount of SPRI beads to remove primer and adapter dimers.
The sequencing data were first demultiplexed based on the barcodes of each sample pooled in the lanes. The data were subjected to a quality control step using FastQC (version 0.11.7), where the low quality reads were discarded from further analysis based on the per base sequence quality and per sequence quality score using the default criteria setting in FastQC(53). Sequencing data were trimmed to remove the adaptors and the terminal CG using the trimmomatic software (v0.38) (54). The reads were aligned to the human genome GRCh38/hg38 (release 93, downloaded from Ensembl) and DNA methylation levels were determined using the BS-Seeker2 pipeline(55) with the aligner bowtie (v1.2.2) and the default settings for the fragment length (20 for lower bound, 500 for upper bound). Samples with less than 5 M total raw reads (3 samples) were excluded from further analyses. On average each sample generated about 36 M total raw reads with 73.7% mappability. Within the study, sequencing data were generated from two sequencing runs, termed batch.

tag: disease state

value: APMB

tag: batch

value: TBS-seq


title: DNAm_Subject_2101111


title: phyAB-RL rep2

city: Shanghai

country: China

description: replicate 2

library_source: transcriptomic

molecule: total RNA

organism: Arabidopsis thaliana

tag: ecotype

tag: genotype

value: 50 μmol/m7/s red light


title: DNAm_Subject_2101081


title: DNAm_Subject_2101101


title: phyB-RL rep2

description: replicate 2

value: phyB

value: 50 μmol/m5/s red light


title: SA04782_S15


title: DNAm_Subject_2101331


title: phyB-RL rep1

description: replicate 1

value: 50 μmol/m4/s red light


title: DNAm_Subject_2101021


title: WT-RL rep2

description: replicate 2

value: WT

value: 50 μmol/m3/s red light


title: DNAm_Subject_2100961


title: SA04816_S17


title: SA04751_S14


title: DNAm_Subject_2100941


title: DNAm_Subject_2100951


title: WT-RL rep1

description: replicate 1

value: 50 μmol/m2/s red light


title: SA04742_S13

value: ARMB


title: DNAm_Subject_2100911


title: WT-D rep2

description: replicate 2

value: dark


title: SA04736_S12


title: DNAm_Subject_2101211


title: SA04821_S18


title: DNAm_Subject_2100901


title: WT-D rep1

description: replicate 1


title: SA04721_S11


title: DNAm_Subject_2100891


title: DNAm_Subject_2100881


title: DNAm_Subject_2100851


title: DNAm_Subject_2100871


title: SA04711_S10


title: DNAm_Subject_2100783


title: SA04697_S9


title: DNAm_Subject_2100712


title: Exp 2 RBFOX1_OE rep 3

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

description:
Exp 2 RBFOX1_OE3
HEK2.counts.txt
HEK2_circCounts.txt

data_processing:
Sequence reads (paired end, 75 bp) were aligned to the human genome sequence (GRCh37/hg19) using STAR (version 2.5.2b).
Reads were quantified using STAR (version 2.5.2b) using --quantMode Gene Counts.
circRNA were quantified using CIRCexplorer2. The parse function from this package was used with the output of the STAR aligner to create a back_spliced_junction.bed file which was then passed to the annotate function to obtain a circularRNA_known.txt file for each sample.
Genome_build: Ensembl Homo sapiens genome (GRCh37)
Supplementary_files_format_and_content: *_counts.txt: Tab-delimited text files with gene expression counts for each sample.
Supplementary_files_format_and_content: *_circCounts.txt: Tab-delimited text files with circRNA counts for each sample.

source_name: HEK293_Flp In/TO △Fox2_Flag_mFox1

extract_protocol:
Total RNA was extracted using the Qiagen miRNeasy mini kit according to manufacturer’s instructions, including an on-column DNase I treatment. RNA integrity was determined using the 2100 Bioanalyzer system.
RNA libraries were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia). The Illumina TruSeq RNA Prep Kit was used to prepared the RNA-Seq libraries which were then sequenced on the Illumina NextSeq500 platform at the Ramaciotti Centre for Genomics UNSW using the paired end protocol to produce R1.fastq and R2.fastq files for each sample.

treatment_protocol: The stable HEK293 line (HEK293_Flp In/TO △Fox2_Flag_mFox1) which was kindly provided from Douglas Black (UCLA) is derived from a Rbfox2 deficient clone and stably expresses HA-Flag-tagged Rbfox1 under an inducible promoter. The stable line was generated using the Flp-In™ T-REx™ System (Life Technologies). Cells were harvested 2-weeks post-induction with 0.5 μg /ml doxycycline.

tag: experiment

tag: cell line

value: HEK293_Flp In/TO <delta>Fox2_Flag_mFox1

tag: treatment

value: Doxycycline

tag: condition

value: RBFOX1 overexpression


title: DNAm_Subject_2100841

value: placenta


title: DNAm_Subject_2100711

value: Female


title: Exp 2 RBFOX1_OE rep 1

description:
Exp 2 RBFOX1_OE1
HEK2.counts.txt
HEK2_circCounts.txt


title: SA04665_S7


title: DNAm_Subject_2100781


title: SA04677_S8


title: DNAm_Subject_2100631


title: DNAm_Subject_2100621


title: Exp 2 Control rep 2

description:
Exp 2 Control2
HEK2.counts.txt
HEK2_circCounts.txt

source_name: HEK293 cell line (parental)

value: Control


title: SA04633_S6


title: DNAm_Subject_2100601

value: Male


title: DNAm_Subject_2100591


title: Exp 2 Control rep 1

description:
Exp 2 Control1
HEK2.counts.txt
HEK2_circCounts.txt


title: SA04632_S5

value: TBS-seq


title: DNAm_Subject_2100571


title: Exp 1 RBFOX1_OE rep 3

description:
Exp 1 RBFOX1_OE3
HEK1.counts.txt
HEK1_circCounts.txt


title: Exp 2 RBFOX1_OE rep 2

description:
Exp 2 RBFOX1_OE2
HEK2.counts.txt
HEK2_circCounts.txt


title: DNAm_Subject_2100472


title: Exp 1 RBFOX1_OE rep 2

description:
Exp 1 RBFOX1_OE2
HEK1.counts.txt
HEK1_circCounts.txt


title: SA04627_S4

value: APMB


title: Exp 1 RBFOX1_OE rep 1

description:
Exp 1 RBFOX1_OE1
HEK1.counts.txt
HEK1_circCounts.txt


title: SA04573_S3


title: DNAm_Subject_2100381


title: Exp 2 Control rep 3

description:
Exp 2 Control3
HEK2.counts.txt
HEK2_circCounts.txt


title: DNAm_Subject_2100301


title: SA04556_S63


title: DNAm_Subject_1700671


title: DNAm_Subject_2100391


title: DNAm_Subject_2100371


title: DNAm_Subject_1700561


title: Exp 1 Control rep 2

description:
Exp 1 Control2
HEK1.counts.txt
HEK1_circCounts.txt

value: Not treated


title: SA04556_S2


title: DNAm_Subject_1700601


title: SA04547_S1


title: DNAm_Subject_1700551


title: DNAm_Subject_1700731


title: DNAm_Subject_1700501


title: Exp 1 Control rep 3

description:
Exp 1 Control3
HEK1.counts.txt
HEK1_circCounts.txt


title: DNAm_Subject_1700443


title: SA04538_S80


title: SA04535_S79


title: Exp 1 Control rep 1

description:
Exp 1 Control1
HEK1.counts.txt
HEK1_circCounts.txt


title: DNAm_Subject_1700442


title: DNAm_Subject_1700441


title: SA04532_S78


title: BA00102: S16-7980/S17-4876

city: San Diego

first: Joan

middle: W

last: Chen

address: 4949 Carroll Canyon Road, Suit 120

institute: Certis Oncology Solution

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Raw fastq files from sequencing runs were processed as follows: Atropos was used to remove the adapter sequences from all the reads; STAR aligner was used to map the reads to the human hg38 genome; RSEM was used to quantitate the reads for each individual gene. Finally, the TPM values were used to represent the mRNA expression of each individual genes.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: breast cancer patients from UConn Health

extract_protocol:
Total RNA was extracted from FFPE samples and quantified using Qubit4 system.
RNA-seq library preparation was performed according to the AmpliSeq for Illumina Transcriptome Human Gene Expression Panel workflow. Library quality control analysis was performed on the Agilent TapeStation System.  Sample libraries passing TapeStation QC were quantified using the Qubit 4 and then normalized, pooled, and loaded into the Illumina NextSeq 500/550 High output 300 cycle v2.5 kit for sequencing of 2x150 paired-end RNA-Seq.

treatment_protocol: neo-adjuvant therapy: neoadjuvant taxane-based chemotherapy

tag: response to nac

value: RD

tag: age

tag: estrogen receptor status

value: P

tag: progesterone receptor status

tag: her2 receptor status

value: N

tag: tumor grage

tag: breast cancer stage

value: breast cancer


title: BA00158: S17-1872/S17-8208

tag: tissue


title: DNAm_Subject_1700431

tag: birthweight (grams)

tag: infant sex

tag: mage (age of mother) (years)

tag: bmi (body mass index)


title: DNAm_Subject_1700412


title: SA04529_S77

tag: disease state

tag: batch


title: DNAm_Subject_1700411


title: BA00100: S16-8145/S17-3516


title: DNAm_Subject_1700343


title: DNAm_Subject_1700341


title: DNAm_Subject_1700342


title: BA00099: S16-8145/S17-3516


title: SA04524_S76


title: SA04516_S75


title: DNAm_Subject_1700281


title: DNAm_Subject_2100691


title: DNAm_Subject_1700242


title: DNAm_Subject_1700331


title: DNAm_Subject_1700282


title: BA00062: S12-6658


title: DNAm_Subject_1700211


title: DNAm_Subject_1700241


title: DNAm_Subject_1700221


title: SA04497_S73


title: SA04503_S74


title: BA00061: S12-6658


title: SA04495_S72


title: DNAm_Subject_1700181


title: DNAm_Subject_1700161


title: SA04471_S71


title: BA00101: S16-7980/S17-4876


title: BA00645: MT1260-083-108

source_name: MT group breast cancer patients

value: pCR


title: DNAm_Subject_1700112


title: SA04469_S70


title: DNAm_Subject_1700102


title: BA00644: MT1260-083-107


title: DNAm_Subject_1700091


title: BA00098: S16-3384/S16-8771


title: DNAm_Subject_1700081


title: SA04464_S68

value: ARMB


title: DNAm_Subject_1700061


title: BA00597: CS15-31258

source_name: breast cancer patients from Hartford Hospital


title: DNAm_Subject_1700011


title: SA04451_S67


title: DNAm_Subject_1600903


title: SA04448_S66


title: DNAm_Subject_1600901


title: BA00596: S15-16563


title: BA00595: CS15-27137


title: DNAm_Subject_1600861


title: SA04448_S62


title: BA00126: HS17-6364(A1)


title: DNAm_Subject_1600752


title: DNAm_Subject_1600751


title: SA04447_S65


title: DNAm_Subject_1600742


title: BA00537: MT1260-083-99


title: DNAm_Subject_1600732


title: SA04468_S69


title: DNAm_Subject_1600722


title: SA04137_S61


title: BA00534: MT1260-083-96


title: BA00599: CS15-33441


title: DNAm_Subject_1600702


title: BA00529: MT1260-083-91


title: DNAm_Subject_1700141


title: DNAm_Subject_1600701


title: DNAm_Subject_1600902


title: DNAm_Subject_1600692


title: BA00519: MT1260-083-81


title: DNAm_Subject_1600662


title: SA04066_S46


title: DNAm_Subject_1600661


title: BA00511: MT1260-92-0004


title: DNAm_Subject_1600652


title: DNAm_Subject_1600641


title: BA00459: MT1260-083-073


title: DNAm_Subject_1600631


title: SA04014_S44


title: BA00449: MT1260-083-063


title: SA04004_S43


title: DNAm_Subject_1600721


title: BA00448: MT1260-083-062


title: DNAm_Subject_1600571


title: DNAm_Subject_1600611


title: SA04096_S48


title: DNAm_Subject_1600561


title: BA00443: MT1260-083-057


title: SA03994_S41


title: DNAm_Subject_1600521


title: DNAm_Subject_1600511


title: SA04095_S47


title: SA03979_S40


title: DNAm_Subject_1600651


title: BA00438: MT1260-083-052


title: DNAm_Subject_1600491


title: BA00430: MT1260-083-044


title: DNAm_Subject_1600351


title: SA04059_S45


title: SA03947_S39


title: DNAm_Subject_1600331


title: BA00429: MT1260-92-0023


title: DNAm_Subject_1600612


title: DNAm_Subject_1600451


title: DNAm_Subject_1600291


title: DNAm_Subject_1600251


title: SA03926_S37


title: SA04002_S42


title: DNAm_Subject_1600241


title: DNAm_Subject_1600151


title: BA00425: MT1260-92-0011


title: SA03912_S36


title: BA00424: MT1260-92-0009


title: DNAm_Subject_1600141


title: DNAm_Subject_1600131


title: BA00441: MT1260-083-055


title: DNAm_Subject_1600111


title: DNAm_Subject_1600381


title: SA03907_S35


title: DNAm_Subject_1600371


title: DNAm_Subject_1501261


title: DNAm_Subject_1501301


title: SA03943_S38


title: SA03886_S59


title: DNAm_Subject_1501171


title: DNAm_Subject_1501191


title: SA03886_S34


title: DNAm_Subject_1501141


title: DNAm_Subject_1501121


title: BA00417: MT1260-92-0028


title: BA00411: MT1260-92-0018


title: DNAm_Subject_1501021


title: DNAm_Subject_1501002


title: BA00410: MT1260-92-0015


title: DNAm_Subject_1500981


title: DNAm_Subject_1500931


title: SA03843_S32


title: SA03879_S33


title: SA03815_S31


title: BA00401: MT1260-92-0001


title: SA03907_S60


title: BA00420: MT1260-92-0032


title: DNAm_Subject_1500911


title: DNAm_Subject_1500841


title: BA00237: MT1260-083-043


title: SA03800_S30


title: BA00418: MT1260-92-0030


title: DNAm_Subject_1500822


title: DNAm_Subject_1500821


title: DNAm_Subject_1500782


title: SA03792_S29


title: BA00232: MT1260-083-038


title: DNAm_Subject_1500781


title: BA00231: MT1260-083-037


title: SA03786_S28


title: DNAm_Subject_1500661


title: BA00227: MT1260-083-033


title: DNAm_Subject_1500601


title: BA00226: MT1260-083-032


title: DNAm_Subject_1500431


title: DNAm_Subject_1400061


title: BA00175: MT1260-24


title: SA03765_S25


title: SA03751_S24


title: DNAm_Subject_1301931


title: DNAm_Subject_1500391


title: DNAm_Subject_1301592


title: SA03739_S23


title: DNAm_Subject_1500491


title: BA00167: MT1260-15


title: SA03771_S26


title: DNAm_Subject_1301591


title: DNAm_Subject_1301541


title: BA00234: MT1260-083-040


title: BA00171: MT1260-19


title: DNAm_Subject_1301401


title: BA00166: MT1260-14


title: DNAm_Subject_1301271


title: SA03736_S22


title: DNAm_Subject_1500731


title: DNAm_Subject_1500681


title: SA03734_S21


title: SA03776_S27


title: DNAm_Subject_1301132


title: DNAm_Subject_1301101


title: SA03727_S20


title: DNAm_Subject_1301131


title: BA00164: MT1260-12


title: DNAm_Subject_1301071


title: DNAm_Subject_1300651


title: SA03716_S58


title: SA03716_S19


title: BA00162: MT1260-10


title: DNAm_Subject_1300571


title: DNAm_Subject_1301031


title: DNAm_Subject_1300672


title: SA03712_S57


title: DNAm_Subject_1300441


title: DNAm_Subject_1300421


title: DNAm_Subject_1300542


title: BA00161: MT1260-08


title: DNAm_Subject_1300412


title: BA00154: S06-549


title: DNAm_Subject_1300541


title: DNAm_Subject_1300391


title: SA03703_S17


title: SA03712_S18


title: BA00144: MT-1260-083-013


title: DNAm_Subject_1300361


title: BA00165: MT1260-13


title: SA03695_S16


title: DNAm_Subject_1300301


title: BA00142: MT-1260-083-011


title: SA03660_S15


title: DNAm_Subject_1300232


title: BA00163: MT1260-11


title: DNAm_Subject_1300231


title: BA00140: MT-1260-083-009


title: SA03635_S14


title: DNAm_Subject_1300201


title: BA00139: MT-1260-083-008


title: DNAm_Subject_1300221


title: SA03618_S13


title: DNAm_Subject_1300171


title: DNAm_Subject_1300161


title: BA00138: MT-1260-083-007


title: DNAm_Subject_1300111


title: DNAm_Subject_1300113


title: SA03596_S12


title: SA03567_S11


title: BA00134: MT-1260-083-003


title: DNAm_Subject_1300011


title: DNAm_Subject_1300071


title: BA00133: MT-1260-083-002


title: DNAm_Subject_1200731


title: DNAm_Subject_1200741


title: DNAm_Subject_1200692


title: SA03556_S10


title: BA00130: MT-1260-03


title: DNAm_Subject_1200691


title: SA03515_S8


title: BA00132: MT-1260-083-001


title: BA00107: CS16-13283(A)


title: DNAm_Subject_1200561


title: DNAm_Subject_1200571


title: SA03505_S7


title: DNAm_Subject_1200671


title: DNAm_Subject_1200522


title: SA03469_S6


title: DNAm_Subject_1200441


title: BA00103: S-16-3042(A1)


title: DNAm_Subject_1200352


title: SA03456_S5


title: BA00093: S12-7292


title: DNAm_Subject_1200351


title: DNAm_Subject_1200321


title: DNAm_Subject_1200281


title: SA03456_S56


title: SA03527_S9


title: DNAm_Subject_1200282


title: BA00085: S07-7023


title: SA03443_S4


title: DNAm_Subject_1200261


title: BA00084: S07-1476


title: DNAm_Subject_1200251


title: SA03436_S55


title: BA00083: S05-6565


title: DNAm_Subject_1200201


title: BA00079: S16-1142


title: DNAm_Subject_1200192


title: SA03436_S3


title: DNAm_Subject_1200521


title: BA00106: S16-7315(A)


title: DNAm_Subject_1200191


title: SA03429_S2


title: DNAm_Subject_1200182


title: DNAm_Subject_1200181


title: SA03423_S1


title: BA00076: S07-611


title: BA00075: S15-6580


title: DNAm_Subject_1200171


title: BA00074: S15-6580


title: DNAm_Subject_1200021


title: DNAm_Subject_1200031


title: ALL cells collected from secondary recipient mice (HCT2)

city: los angeles

first: Du

last: Jiang

state: ca

address: 1425 san pablo st bcc 305

department: stem cell

institute: university of southern california

data_processing:
raw fastq files were generated by Illumina bcl2fastq software with default parameters
fastq files of each sample were processed separately using cellranger software (v2.1.0) "cellranger count" with default settings
Genome_build: hg19
Supplementary_files_format_and_content: HDF5 file containing UMI matrix of each gene in each cell

source_name: B-cell acute lymphoblast leukemia cells

extract_protocol:
Chromium Single Cell 3’ Library (10X Genomics, V2)
single cell RNAseq

tag: developmental stage

value: adult

tag: cell type

value: ALL cells (GFP+hCD45+)

tag: cell source

value: secondary recipient NSG mice


title: ALL cells collected from secondary recipient mice (HCT3)


title: DNAm_Subject_1101171


title: DNAm_Subject_1200011


title: ALL cells collected from primary recipient mice (HCT1)

value: primary recipient NSG mice


title: BA00073: S15-3014

tag: response to nac


title: DNAm_Subject_1101161

value: placenta


title: BA00070: S14-3867

tag: age


title: TL_D30 rep 2

city: La Jolla

first: Priya

last: Nayak

state: CA

address: 9500 Gilman Drive

institute: University of California San Diego

description:
TL_TPM.csv
TL_geneCounts.csv

data_processing:
Raw read quality assessed with FASTQC
Raw reads aligned to human cDNA, ncRNA transcriptome with Salmon (Patro et al. Nat Methods, 2017)
Summation of transcript count to gene counts carried out with tximport (Sonneson et al. F1000Research, 2015)
Differential expression analysis with DESeq2 (Love et al. Genome Biology, 2014)
Genome_build: GRCh38
Supplementary_files_format_and_content: *_TPM.csv files contain TPM normalized gene counts, for all timepoints and replicates for each cell line
Supplementary_files_format_and_content: *_geneCounts.csv files contain raw gene counts, for all timepoints and replicates for each cell line

molecule: polyA RNA

source_name: hiPSC line TL

growth_protocol: Three distinct hiPSC lines were cultured in parallel: Pluripotent hiPSC colonies were plated onto six-well plates that had been coated with Matrigel (Corning) according to manufacturer’s instructions overnight at 4C. Maintenance media mTeSR1 (STEMCELL Tech) was refreshed daily. hiPSCs were passaged at ~70% confluence using ReLeSR (STEMCELL Tech).

extract_protocol:
RNA was harvested using TRIzol reagent
Library prep carried out with the Illumina TruSeq stranded mRNA kit for poly-A selection

treatment_protocol: Pluripotent hiPSC colonies were seeded for differentiation by adding 500uL Versene (0.5 mM EDTA solution, Gibco) per well in a six-well plate, incubating at 37C for nine minutes to detach cells as single cells. These were then replated as single cells on Matrigel coated plates as above. Undifferentiated hiPSCs were plated at a seeding density of 20,000 cells per square centimeter in mTeSR with 1% penicillin-streptomycin (Gibco) and 2uM TZV (Selleck Chemicals) for 24 hours to allow for attachment. Differentiation was induced 24 hours after plating following published protocol in Generation of human muscle fibers and satellite-like cells from human pluripotent stem cells in vitro. by Chal et al, Nature Protocols, 2016

tag: treatment

value: Myogenic induction according to (Chal et al. Nat Prot, 2016)

tag: timepoint

value: Day 30


title: DNAm_Subject_1200232

value: Male


title: DNAm_Subject_1101142


title: DNAm_Subject_1101141


title: BA00069: S14-3867

tag: estrogen receptor status

tag: progesterone receptor status

tag: her2 receptor status


title: DNAm_Subject_1101131

tag: tissue

value: Female


title: TL_D30 rep 1

description:
TL_TPM.csv
TL_geneCounts.csv


title: DNAm_Subject_1101091

tag: birthweight (grams)


title: DNAm_Subject_1101092

tag: infant sex


title: TL_D25 rep 2

description:
TL_TPM.csv
TL_geneCounts.csv

value: Day 25


title: BA00068: S14-3295

tag: tumor grage

tag: breast cancer stage


title: BA00067: S14-3295


title: DNAm_Subject_1101081

tag: mage (age of mother) (years)

tag: bmi (body mass index)


title: TL_D25 rep 1

description:
TL_TPM.csv
TL_geneCounts.csv


title: DNAm_Subject_1200172


title: BA00065: S13-2879


title: DNAm_Subject_1101042


title: DNAm_Subject_1101041


title: DNAm_Subject_1101001


title: DNAm_Subject_1100891


title: DNAm_Subject_1100901


title: DNAm_Subject_1100881


title: BA00027: S11-426 / S107914/S11-3368


title: DNAm_Subject_1100872


title: DNAm_Subject_1100852


title: DNAm_Subject_1100853


title: BA00655: MT1260-083-118


title: TL_D19 rep 1

description:
TL_TPM.csv
TL_geneCounts.csv

value: Day 19


title: BA00024: S10-3362

value: RD


title: TL_D16 rep 2

description:
TL_TPM.csv
TL_geneCounts.csv

value: Day 16


title: TL_D19 rep 2

description:
TL_TPM.csv
TL_geneCounts.csv


title: BA00028: S11-426 / S107914/S11-3368

value: P

value: N


title: DNAm_Subject_1100841


title: TL_D16 rep 1

description:
TL_TPM.csv
TL_geneCounts.csv


title: DNAm_Subject_1100791


title: TL_D12 rep 2

description:
TL_TPM.csv
TL_geneCounts.csv

value: Day 12


title: BA00653: MT1260-083-116

value: breast cancer


title: TL_D12 rep 1

description:
TL_TPM.csv
TL_geneCounts.csv


title: BA00654: MT1260-083-117

value: pCR


title: DNAm_Subject_1100751


title: DNAm_Subject_1100711


title: DNAm_Subject_1100691


title: TL_D8 rep 2

description:
TL_TPM.csv
TL_geneCounts.csv

value: Day 8


title: BA00651: MT1260-083-114


title: DNAm_Subject_1100601


title: TL_D8 rep 1

description:
TL_TPM.csv
TL_geneCounts.csv


title: DNAm_Subject_1100551


title: BA00648: MT1260-083-111


title: DNAm_Subject_1100521


title: TL_D6 rep 2

description:
TL_TPM.csv
TL_geneCounts.csv

value: Day 6


title: BA00647: MT1260-083-110


title: DNAm_Subject_1100511


title: DNAm_Subject_1100471


title: DNAm_Subject_1100462


title: TL_D6 rep 1

description:
TL_TPM.csv
TL_geneCounts.csv


title: BA00643: MT1260-083-106


title: DNAm_Subject_1100461


title: TL_D3 rep 2

description:
TL_TPM.csv
TL_geneCounts.csv

value: Day 3


title: DNAm_Subject_1100391

value: placenta


title: TL_D3 rep 1

description:
TL_TPM.csv
TL_geneCounts.csv

value: Myogenic induction according to (Chal et al. Nat Prot, 2016)


title: BA00639: MT1260-083-102


title: DNAm_Subject_1100361


title: BA00640: MT1260-083-103


title: DNAm_Subject_1100112


title: BA00638: MT1260-083-101


title: BA00636: MT1260-081-001


title: DNAm_Subject_1100611


title: T-ALL_sample_MOL_JU

city: Paris

first: Vahid

last: Asnafi

address: 149 rue de Sèvres

country: France

institute: Universite de Paris (Descartes)

description: genomic data from T-ALL leukemic blasts

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

scan_protocol: Standard Illumina Protocol

data_processing:
Raw IDAT files were processed with RnBeads bioconductor package and background normalized to produce methylation beta values
Mat_processed.tsv includes normalized data matrix includes normalized (NOOB) beta values
Mat_signal_intesities.tsv includes Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Leukemic Bone Marrow

label_protocol: Standard Illumina Protocol

extract_protocol: DNA isolation using Qiagen blood and tissue isolation kit according to manufacturer's protocol

tag: gender

tag: diagnosis

value: T-ALL

value: T-ALL Bone Marrow


title: TL_D0 rep 2

description:
TL_TPM.csv
TL_geneCounts.csv

value: Day 0


title: T-ALL_sample_GEN_EE

description: genomic data from T-ALL leukemic blasts

value: Female


title: SCVI_D30 rep 2

description:
SCVI_TPM.csv
SCVI_geneCounts.csv

source_name: hiPSC line SCVI15

value: Day 30


title: BA00608: CS15-13295

value: RD


title: SCVI_D30 rep 1

description:
SCVI_TPM.csv
SCVI_geneCounts.csv


title: T-ALL_sample_CON_NI

description: genomic data from T-ALL leukemic blasts

value: Male


title: BA00601: CS15-16522


title: T-ALL_sample_731

description: genomic data from T-ALL leukemic blasts


title: SCVI_D25 rep 2

description:
SCVI_TPM.csv
SCVI_geneCounts.csv

value: Day 25


title: DNAm_Subject_1100111


title: BA00600: CS15-29137

value: P

value: N


title: TL_D0 rep 1

description:
TL_TPM.csv
TL_geneCounts.csv


title: DNAm_Subject_1100381


title: SCVI_D25 rep 1

description:
SCVI_TPM.csv
SCVI_geneCounts.csv


title: BA00586: HS16-20858

value: breast cancer


title: BA00120: HS17-1008(A2)


title: BA00535: MT1260-083-97


title: SCVI_D19 rep 2

description:
SCVI_TPM.csv
SCVI_geneCounts.csv

value: Day 19


title: SCVI_D16 rep 2

description:
SCVI_TPM.csv
SCVI_geneCounts.csv

value: Day 16


title: SCVI_D12 rep 2

description:
SCVI_TPM.csv
SCVI_geneCounts.csv

value: Day 12


title: BA00531: MT1260-083-93

value: pCR


title: SCVI_D16 rep 1

description:
SCVI_TPM.csv
SCVI_geneCounts.csv


title: SCVI_D12 rep 1

description:
SCVI_TPM.csv
SCVI_geneCounts.csv


title: BA00530: MT1260-083-92


title: BA00526: MT1260-083-88


title: BA00525: MT1260-083-87


title: T-ALL_sample_674

description: genomic data from T-ALL leukemic blasts


title: BA00527: MT1260-083-89


title: SCVI_D8 rep 2

description:
SCVI_TPM.csv
SCVI_geneCounts.csv

value: Day 8


title: SCVI_D8 rep 1

description:
SCVI_TPM.csv
SCVI_geneCounts.csv

value: Myogenic induction according to (Chal et al. Nat Prot, 2016)


title: T-ALL_sample_DUB_GL

description: genomic data from T-ALL leukemic blasts

value: T-ALL


title: BA00523: MT1260-083-85


title: T-ALL_sample_673

description: genomic data from T-ALL leukemic blasts

value: T-ALL Bone Marrow


title: T-ALL_sample_672

description: genomic data from T-ALL leukemic blasts


title: BA00522: MT1260-083-84


title: BA00520: MT1260-083-82


title: SCVI_D3 rep 2

description:
SCVI_TPM.csv
SCVI_geneCounts.csv

value: Day 3


title: BA00598: CS15-30734


title: SCVI_D19 rep 1

description:
SCVI_TPM.csv
SCVI_geneCounts.csv


title: BA00518: MT1260-083-80


title: SCVI_D0 rep 2

description:
SCVI_TPM.csv
SCVI_geneCounts.csv

value: Day 0


title: SCVI_D0 rep 1

description:
SCVI_TPM.csv
SCVI_geneCounts.csv


title: BA00517: MT1260-083-79


title: LEPCC3_D30 rep 2

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv

source_name: hiPSC line LEPCC3

value: Day 30


title: BA00515: MT1260-083-77


title: BA00512: MT1260-92-0017


title: LEPCC3_D30 rep 1

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv


title: BA00460: MT1260-083-074


title: LEPCC3_D25 rep 1

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv


title: LEPCC3_D19 rep 2

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv


title: BA00516: MT1260-083-78


title: SCVI_D6 rep 2

description:
SCVI_TPM.csv
SCVI_geneCounts.csv

value: Day 6


title: SCVI_D6 rep 1

description:
SCVI_TPM.csv
SCVI_geneCounts.csv


title: BA00457: MT1260-083-071


title: T-ALL_sample_616

description: genomic data from T-ALL leukemic blasts

value: Male


title: LEPCC3_D16 rep 1

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv


title: SCVI_D3 rep 1

description:
SCVI_TPM.csv
SCVI_geneCounts.csv


title: LEPCC3_D19 rep 1

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv


title: LEPCC3_D16 rep 2

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv


title: BA00458: MT1260-083-072

value: RD


title: BA00454: MT1260-083-068


title: LEPCC3_D12 rep 1

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv


title: BA00452: MT1260-083-066

value: P


title: T-ALL_sample_629

description: genomic data from T-ALL leukemic blasts

value: Female


title: LEPCC3_D8 rep 2

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv


title: BA00451: MT1260-083-065

value: N

value: breast cancer


title: BA00450: MT1260-083-064


title: LEPCC3_D6 rep 2

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv


title: LEPCC3_D25 rep 2

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv

value: Day 25


title: BA00514: MT1260-083-76


title: BA00447: MT1260-083-061


title: BA00446: MT1260-083-060


title: LEPCC3_D6 rep 1

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv


title: LEPCC3_D3 rep 2

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv


title: BA00456: MT1260-083-070


title: BA00445: MT1260-083-059


title: LEPCC3_D0 rep 2

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv


title: BA00440: MT1260-083-054


title: LEPCC3_D0 rep 1

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv


title: T-ALL_sample_554

description: genomic data from T-ALL leukemic blasts


title: BA00455: MT1260-083-069


title: BA00437: MT1260-083-051


title: Dialysis_15 [S26]

city: North Chicago

first: Ameya

middle: S

last: Kulkarni

state: Illinois

address: 1 N Waukegan Road

department: Genomics Research Center

institute: AbbVie

data_processing:
Total RNA was sequenced on Illumina HiSeq 4000 system at Novogene Corporation, Chula Vista, CA, using a paired-end 150 bp dual-indexing protocol. Raw fastq reads were passed through quality control using FastQC (v0.11.4) and the results were compiled using MultiQC (v1.7).
Reads that were detected for adapter contamination were subjected to adapter trimming, while low quality and too short reads were filtered using default parameters in fastp (v0.19.4)
The reads that passed quality control were aligned to GRCh38 primary build of the reference human genome with transcript annotations (gencode.v29.annotation.gtf) obtained from GENCODE, using the STAR aligner (v2.6.1b)
The transcripts were quantified using RNA-Sequencing by Expectation Maximization- RSEM (v1.3.0)
All statistical analysis for the gene expression data were carried out using the R statistical software (R-4.0.2)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts for each sample (generated using RSEM)

source_name: Dialysis_vastus lateralis muscle

extract_protocol:
Approximately 35 mg of muscle was subjected to bead homogenization in Qiazol and RNA purified using miRNeasy Mini Kits and stored at -80 C.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject id

tag: group

value: Dialysis

tag: Sex

tag: race

value: black

value: vastus lateralis muscle


title: CKD_15 [S25]

source_name: CKD_vastus lateralis muscle

value: CKD

tag: age


title: LEPCC3_D12 rep 2

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv

tag: treatment

value: Myogenic induction according to (Chal et al. Nat Prot, 2016)

tag: timepoint

value: Day 12


title: T-ALL_sample_548

description: genomic data from T-ALL leukemic blasts

value: T-ALL

value: T-ALL Bone Marrow


title: BA00436: MT1260-083-050

tag: response to nac

tag: estrogen receptor status

tag: progesterone receptor status

tag: her2 receptor status


title: LEPCC3_D8 rep 1

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv

value: Day 8


title: CKD_14 [S22]

tag: tissue


title: BA00432: MT1260-083-046

tag: tumor grage

tag: breast cancer stage


title: Dialysis_14 [S23]


title: BA00428: MT1260-92-0019

value: pCR


title: BA00435: MT1260-083-049


title: Dialysis_13 [S21]


title: BA00431: MT1260-083-045


title: CKD_12 [S20]


title: CKD_11 [S19]

value: Male

value: non-black


title: BA00442: MT1260-083-056

value: P


title: LEPCC3_D3 rep 1

description:
LEPCC3_TPM.csv
LEPCC3_geneCounts.csv

value: Day 3


title: Dialysis_10 [S18]


title: BA00423: MT1260-92-0035

value: RD

value: N


title: BA00426: MT1260-92-0012

value: breast cancer


title: BA00422: MT1260-92-0034


title: CKD_10 [S17]


title: CKD_8 [S15]


title: BA00421: MT1260-92-0033


title: Control_7 [C9]

source_name: Control_vastus lateralis muscle

value: Control

value: Female


title: CKD_9 [S16]

value: black

value: vastus lateralis muscle


title: BA00419: MT1260-92-0031


title: BA00439: MT1260-083-053


title: BA00415: MT1260-92-0026


title: BA00414: MT1260-92-0024


title: Control_4 [C5]


title: Control_6 [C8]


title: Control_3 [C4]


title: BA00412: MT1260-92-0021


title: Control_2 [C2]


title: BA00413: MT1260-92-0022


title: BA00409: MT1260-92-0014


title: BA00427: MT1260-92-0016


title: Control_1 [C1]


title: BA00408: MT1260-92-0013


title: BA00407: MT1260-92-0010


title: SA05572

data_processing:
Read quality was checked using FastQC (version 0.11.7)
Reads with the adaptors and the terminal CG were trimmed using the trimmomatic software (v0.38)
Reads aligned using BS-Seeker2 pipeline with the aligner bowtie (v1.2.2)
Genome_build: cohort1(Hg19); cohort2(Hg38)
Supplementary_files_format_and_content: [CGfinal files] chromosome, dinucleotide, position, methylated counts, total counts, methylation frequency, 95% confidence interval for methylation frequency

tag: disease state

value: APMB

tag: batch


title: SA05682


title: SA05537


title: BA00406: MT1260-92-0008


title: BA00405: MT1260-92-0007


title: SA05519

value: ARMB


title: BA00404: MT1260-92-0006


title: BA00403: MT1260-92-0003


title: Control_5 [C7]


title: SA05444


title: SA05467


title: BA00398: MT1260-061-09


title: BA00236: MT1260-083-042


title: BA00402: MT1260-92-0002


title: BA00235: MT1260-083-041


title: BA00229: MT1260-083-035


title: SA05423


title: T-ALL_sample_383

description: genomic data from T-ALL leukemic blasts

tag: gender

tag: diagnosis

value: T-ALL


title: SA05177


title: BA00224: MT1260-083-030


title: SA05432


title: BA00223: MT1260-083-029


title: BA00222: MT1260-083-028


title: SA04677


title: SA04697


title: T-ALL_sample_439

description: genomic data from T-ALL leukemic blasts

value: T-ALL Bone Marrow


title: SA04665


title: BA00221: MT1260-083-027


title: T-ALL_sample_437

description: genomic data from T-ALL leukemic blasts


title: SA04629


title: BA00220: MT1260-083-026


title: SA04573


title: BA00219: MT1260-083-025


title: T-ALL_sample_234

description: genomic data from T-ALL leukemic blasts


title: 1044 DAY 5 MTZ Replicate 3

city: Houston

first: George

last: Eisenhoffer

state: TX

address: 1515 Holcombe Blvd., Unit 1010

department: Genetics

institute: The University of Texas MD Anderson Cancer Center

data_processing:
FastQC (version 0.11.8)used for quality control
Trimmomatic (version 0.33) trim reads and remove adaptors
HiSat2 (2.0.4) aligned to zebrafish genome (GRCz11)
Samtools (1.8) sort and index
Featurecounts (1.6.3) count reads
Genome_build: GRCz11
Supplementary_files_format_and_content: Featurecounts output

organism: Danio rerio

source_name: tissue repair after induced epithelial cell loss (18hr after MTZ washout, 5 dpf larval zebrafish)

growth_protocol: Day 4, 5 or 6 zebrafish embryos

extract_protocol:
15-30 individual fish pooled in Trizol.  Rneasy kit (Qiagen 74104) for extraction, on-column DNAse treatment (Qiagen 79254)
TrueSeq Stranded Total RNA-seq

value: Whole animal

tag: line

value: Metronidazole

tag: time point

value: DAY 5


title: SA04556


title: 1044 DAY 5 MTZ Replicate 2


title: BA00218: MT1260-083-024


title: SA04538


title: SA04736


title: TCRp_2

description: genomic data from Double Positive CD4+ CD8+ TCR+ CD3+ thymic cells rep-2

source_name: Healthy Thymus

value: normal

value: Normal Thymic cell type


title: 1044 DAY 5 MTZ Replicate 1


title: BA00217: MT1260-083-023

value: P


title: 1044 DAY 4 MTZ Replicate 3

source_name: induced epithelial cell loss (5hr MTZ, 4 dpf larval zebrafish)


title: SA04532

source_name: Peripheral blood


title: SA04632


title: TCRp_1

description: genomic data from Double Positive CD4+ CD8+ TCR+ CD3+ thymic cells rep-1


title: SA04524


title: BA00216: MT1260-083-022

value: RD


title: 1044 DAY 4 MTZ Replicate 2

value: DAY 4


title: TCRn_2

description: genomic data from Double Positive CD4+ CD8+ TCR- CD3- thymic cells rep-2


title: 1044 DAY 4 MTZ Replicate 1


title: TCRn_1

description: genomic data from Double Positive CD4+ CD8+ TCR- CD3- thymic cells rep-1


title: SPo8_2

description: genomic data from mature CD8 positive thymic cells rep-2


title: SA04516


title: BA00152: MT-1260-083-021

value: N

value: breast cancer


title: SA04503


title: WT DAY 5 Replicate 3

source_name: larval zebrafish under homeostatic conditions (5 dpf)

value: AB


title: BA00151: MT-1260-083-020


title: BA00148: MT-1260-083-017

value: pCR


title: WT DAY 5 Replicate 2


title: SPo8_1

description: genomic data from mature CD8 positive thymic cells rep-1


title: SA04451


title: SA04464


title: WT DAY 5 Replicate 1


title: SPo4_2

description: genomic data from mature CD4 positive thymic cells rep-2


title: BA00147: MT-1260-083-016


title: SPo4_1

description: genomic data from mature CD4 positive thymic cells rep-1


title: SA04448


title: BA00146: MT-1260-083-015


title: WT DAY 4 Replicate 3

source_name: larval zebrafish under homeostatic conditions (4 dpf)


title: SA04447


title: WT DAY 4 Replicate 2


title: BA00145: MT-1260-083-014


title: ISP_2

description: genomic data from Immature Simple positive CD4+ thymic cells rep-2


title: ISP_1

description: genomic data from Immature Simple positive CD4+ thymic cells rep-1


title: SA04420


title: BA00143: MT-1260-083-012


title: SA04407


title: WT DAY 4 Replicate 1


title: AM-KO rep2

city: Tianjin

first: li

last: tengda

address: Heping

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
SOAPnuke software used for filtering;
HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts)  software was used for RNA-seq reads alignment to reference genome
Use sequence alignment software to compare the clean reads after quality control to the reference genome, so that the gene/transcript expression in the sample can be quantified. At the same time, the overall analysis of this transcriptome sequencing, including the randomness of the transcripts
Use sequence alignment software to compare the clean reads after quality control to the reference gene set, so that the gene/transcript expression in the sample can be quantified. At the same time, the overall analysis of this transcriptome sequencing, including the coverage and distribution of the transcripts.
Use perl scripts to perform sequencing saturation analysis, which can determine whether the amount of sequencing data meets the requirements to a certain extent. As the amount of sequencing (the number of Reads) increases, the number of genes detected also increases. When the amount of sequencing reaches a certain interval, the growth rate of the number of detected genes tends to be flat, indicating that the number of detected genes tends to be saturated. At this time, the sequencing volume meets the requirements.
Genome_build: NCBI_GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: lung

extract_protocol:
We sort AM from the lung of ko mice and wt mice(2:2) with purify more than 90%
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: lung

tag: cell type

value: alveolar macrophage

value: post natal day 10

tag: genotype


title: BA00141: MT-1260-083-010

source_name: MT group breast cancer patients

tag: age


title: CD34_1

description: genomic data from CD34 positive thymic cells rep-1


title: SA04374

value: ARMB


title: BA00137: MT-1260-083-006

tag: response to nac


title: BA00136: MT-1260-083-005

tag: estrogen receptor status


title: SA04294

value: APMB


title: AM WT rep2


title: AM-KO rep1


title: SA04266


title: AM WT rep1


title: DDX56 RNAi intact animals

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

description: 3 RNAi feeds of ddx56, stem cells collected 3 days after last feed

data_processing:
Base calls and demultiplexing was performed with Illumina bcl2fastq2 version 2.20
Untrimmed reads were aligned to the transcritpome associated with BioProject 215411 using the program Bowtie2 version 2.2.4.  Raw counts were extracted from resulting SAM files and normalized to the number of mapped reads to calculate Counts Per Million reads (CPM).
Differentially expressed genes were identified by fold-change in expression compared to wild-type X1 cells previously published in GEO accessions: GSE37910, GSE68581
Both the X1l3r1 and X1l5r1 are from GSM1675833 (two runs/replicates), CCBR X1 is from GSM929778, and 'WT X1 RPM +1' is the average of all 3 replicates (X1l3r1, X1l5r1, CCBR X1 included in the 'WT X1' spreadsheet )
Genome_build: NCBI BioProject PRJNA215411  SmedASXL_transcripts_20130210.nt
Supplementary_files_format_and_content: Excel, raw CPM counts with a pseudocount of +1 added to every number

organism: Schmidtea mediterranea

source_name: Wildtype animals (>100 animals)

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.  Organisms were starved for 1 week prior to starting RNAi treatment.

extract_protocol:
All tissue samples were RNA extracted in Trizol reagent, and RNA quality was analyzed on a bioanalyzer.  RNA samples were library prepped using Illumina's Truseq Library preps, which included polyA selection.
Illumina TruSeq library prep kit with v4 chemistry.

treatment_protocol: Smed-ddx56(RNAi) animals were fed 3 times over 6 days. Cells and RNA was collected 3 days after the last feed. Samples were sequenced to a depth of >250 million paired-end 125bp reads.

value: Asexual CIW4

value: Approximately 500,000 FACS purified X1 cells (high hoechst)

tag: treatment

value: DDX56 RNAi


title: SA04233


title: BA00129: MT-1260-02

tag: progesterone receptor status

tag: her2 receptor status


title: SA04113


title: BA00135: MT-1260-083-004

tag: tumor grage

tag: tissue


title: vim1-3_23C_C

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

institute: CNRS

data_processing:
Sequenced reads were trimmed using trimmomatic V0.36 to remove adapters and low quality bases. Robosomal RNA where removed using SortMeRNA (v2.1)
trimmed reads were aligned to the TAIR10 genome using STAR (2.5.2b)
Reads were counted using featureCounts from subreads package (v1.6.5) using strand specific mode.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sampla

source_name: seedlings

growth_protocol: Seeds were surface-sterilized by treatments with 70% EtOH and 5% hypochloryte-1% SDS, washed and stratified at 4°C for 2 days to obtain homogeneous germination. Seedlings were grown at 23°C or 29°C on solid half-strength Murashige and Skoog (MS/2) medium (Duchefa), under long day conditions (16h light, 95μE.m-2.sec-1/8h dark).

extract_protocol:
Total RNA was isolated using Plant RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq RNA

treatment_protocol: Seedlings were grown either at 23°C or 29°C according to the sample

tag: developmental stage

value: seedlings


title: vim1-3_23C_B


title: BA00115: WT169906169(A1)

source_name: breast cancer patients from Hartford Hospital

tag: breast cancer stage


title: SA04066

tag: disease state

tag: batch


title: BA00112: HS16-20329(A1)


title: SA04014


title: 35SAPOLO_23C_C


title: CD34_2

description: genomic data from CD34 positive thymic cells rep-2

tag: gender

tag: diagnosis

value: normal

value: Normal Thymic cell type


title: BA00110: WT169905541(A2)

value: RD

value: P


title: 35SAPOLO_23C_B


title: SAMPLE 5: Sham OC#2

type: RNA

city: Hong Kong SAR

first: Jin

last: Liu

address: 7 Baptist University Road, Kowloon Tong

department: TMBJ

institute: Hong Kong Baptist University

data_processing:
The normalization and all the data analysis was performed using the manufacturer's qPCR analysis templates https://systembio.com/wp-content/uploads/Mouse_miRNome_v14_2.xls
For the normalization it uses the mouse U6 snRNA.
Target miRNA signals were normalized to the average U6 snRNA signals of OCs; 2^-deltaCt, where deltaCt = (Ct_Target - Ct_U6 average)]
All deltadeltaCt based fold-change were calculated from the uploaded raw threshold cycle data automatically by the templates.
Matrix normalized worksheet reports normalized signal (against U6).
Fold Change worksheet reports test/control (i.e., ACLT OC/Sham OC) ratios.

label: SYBR Green

source_name: Bone marrow-derived OSCAR+CTR+ osteoclasts

label_protocol: Reverse transcription was performed using the QuantiMir RT Kit (System Biosciences) according to the manufacturer's instructions Real-time qPCR was performed (Applied Biosystems ViiA7) using standard run conditions (40 cycles at 95oC for 15 seconds and 60oC for 60 seconds.)

growth_protocol: The mice received ACLT or Sham operation for 2 weeks.

extract_protocol: Total RNA was extracted with Trizol Reagent

treatment_protocol: The osteoclasts (Ocs) were isolated from bone marrow cells of ACLT mice or Sham mice by magnetic-activated cell sorting.

value: OSCAR+CTR+ osteoclasts


title: SAMPLE 6: Sham OC#3


title: SAMPLE 3: ACLT OC#3


title: BA00104: CH16-2332(A)

value: N

value: breast cancer


title: SA04002


title: BA00096: S10-7089

source_name: breast cancer patients from UConn Health

value: pCR


title: SAMPLE 2: ACLT OC#2


title: Col0_29C_C

value: wild type


title: 35SAPOLO_23C_A


title: SA03994


title: BA00095: S10-7089


title: SAMPLE 1: ACLT OC#1


title: PLC_RNAseq

city: Hangzhou

first: Xushen

last: Xiong

state: Zhejiang

address: Wenyi Road West

department: Medical Center

institute: Zhejiang University

description:
NA
PLC.TE.xls

data_processing:
Raw sequencing reads produced from m1A-seq were firstly subjected to Trim_galore (version 0.3.7. http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for quality control and adaptor trimming. The minimum quality threshold was set to 20, and the minimum length required for reads after trimming was 30 nt. The remaining reads were further processed by removing the first 10 nt random barcode in the 5’ end. As for the ribosome profiling (Ribo-seq) data and the corresponding RNA-seq data, reads with a quality lower than 20 were discarded, and the adaptor in 3’ end was trimmed. Processed reads with a length ranging from 25 nt to 35 nt in the ribosome profiling sample were kept for further analysis.
Processed reads from m1A-seq were mapped to tRNA sequences, which was downloaded from UCSC Table Browser, using BWA-MEM (version 0.7.17-r1188) with default parameters. The processed reads from Ribo-seq were mapped to human transcriptome (Refseq annotation, downloaded from UCSC Table Browser) using BWA-MEM (version 0.7.17-r1188) with default parameters.
For m1A-seq analysis, reads mapping to an identical position of reference were considered as PCR duplications if their 10 nt random barcodes were the same, and only one of these reads was kept.
Samtools mpileup (1.8) was used to extract the reads mapping of every nucleotide in the tRNA transcriptome.
Mismatch rate was calculated using in-house scripts. RPKM was calculated using in-house scripts following the definition of RPKM, translation efficiency (TE) were then calculated following: TE=RPKM(Riboseq)/RPKM(RNAseq).
Genome_build: hg19
Supplementary_files_format_and_content: Mismatch rate file in tab-delimited format; containing the mismatch rate for every nucleotide in the tRNA transcriptome; For Riboseq data, the processed files are translation efficiency file in tab-demilited format.
Supplementary_files_format_and_content: PLC_m1Aseq.mismatch.xls: Mismatch rate file in tab-delimited format
Supplementary_files_format_and_content: PLCStem_m1Aseq.mismatch.xls: Mismatch rate file in tab-delimited format
Supplementary_files_format_and_content: AlkB-PLC_m1Aseq.mismatch.xls: Mismatch rate file in tab-delimited format
Supplementary_files_format_and_content: AlkB-PLCStem_m1Aseq.mismatch.xls: Mismatch rate file in tab-delimited format
Supplementary_files_format_and_content: PLC.TE.xls: Translation efficiency file in tab-demilited format
Supplementary_files_format_and_content: PLC_stem.TE.xls: Translation efficiency file in tab-demilited format

source_name: human PLC cell line

growth_protocol: Human hepatocellular carcinoma (HCC) cell line PLC/PRF/5 was maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 100 μg/ml penicillin G, and 100 U/ml streptomycin (Invitrogen, NY, USA).

extract_protocol:
For m1A-seq, total RNA was isolated from cell lines by Trizol(invitrogen).<200 nt fraction RNA was enriched from total RNA with size selection using Megaclear kit (invitrogen), then was collected from the flow through.
For m1A-seq, RNA samples were dephosphorylated with PNK (NEB) and ligated to 3’ RNA linker using T4 RNA ligase2, truncated KQ (NEB). Reverse transcription was carried using different reverse transcriptase for different samples.  5’ adaptor was ligated to cDNA and then amplified by PCR. PCR products were purified by 8% TBE gel

treatment_protocol: We sorted liver CSCs (CD13+CD133+) and non-CSCs (CD13-CD133-). For cell sorting, cocktail PE-conjugated anti-human CD133 and FITC-conjugated anti-human CD13 antibodies were incubated with HCC PLC/PRF/5 cells, followed by sorting with FACS Aria III (BD Immunocytometry Systems, San Jose, CA, USA).

value: Normal PLC cells

tag: library strategy

value: RNA seq


title: BA00094: S12-7978


title: PLCStem_RNAseq

description:
NA
PLC_stem.TE.xls

tag: cell type

value: PLC stem cells


title: SA03979

value: ARMB


title: Col0_29C_A

tag: genotype


title: vim1-3_23C_A


title: SA03947

value: APMB


title: PLCStem_ribo

description:
NA
PLC_stem.TE.xls

value: Ribosome profiling


title: BA00090: S09-3814

tag: age


title: PLC_ribo

description:
NA
PLC.TE.xls


title: Col0_23C_C


title: SA03943


title: SAMPLE 4: Sham OC#1


title: sample_3

city: Lisboa

first: Arsenio

middle: M.

last: Fialho

state: Lisboa

address: Av. Rovisco Pais, 1

country: Portugal

institute: Institute for Bioengineering and Biosciences, Instituto Superior Técnico

description:
sample-2
C-vs-S_results.txt
C vs S raw.txt

data_processing:
RNA sequencing was conducted as a service provided by Admera Health Biopharma Services (South Plainfield, NJ, USA), using a validated Transcriptomic Analysis Pipeline
Before alignment of sequence reads, quality check (FastQC), removal of adapter content (used during sequencing) and quality thresholding (remove any bad quality reads (Phred Score < 30)), were performed
The RNA-Seq reads were mapped against the genome and annotations of B. cenocepacia J2315 (GCF_000009485.1) to identify transcripts
Genome_build: GCF_000009485.1
Supplementary_files_format_and_content: C-vs-S_results.txt:  normalized abundance measurements
Supplementary_files_format_and_content: C vs S raw.txt:  raw counts of sequencing reads

organism: Burkholderia cenocepacia

source_name: GPMV adherent

growth_protocol: Cells were grown in LB medium (initial OD640 0.1) at 37ºC with orbital agitation at 250 rpm, for 6 h until reaching a mid-exponential phase of growth. Cells were pelleted and frozen at -80ºC until RNA extraction.

extract_protocol:
RNeasy mini kit (Qiagen), according the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols. Library prep kit: TruSeq Stranded RNA with rRNA Depletion

treatment_protocol: Cells in mid-exponential phase were allow to adhere to a confluent monolayer of GPMVs (giant plasma membrane vesicles) derived from 16HBE14o- human bronchial epithelial cell line for 30 min, at 37ºC, 5% CO2

tag: strain

value: wild-type

value: GPMV-adhesion


title: BA00080: S16-7463/S17-3374

tag: response to nac

tag: estrogen receptor status


title: SA03926


title: SA04004


title: BA00081: S16-7296

tag: progesterone receptor status


title: BA00071: S14-8083

tag: her2 receptor status


title: sample_2

description:
sample-1
C-vs-S_results.txt
C vs S raw.txt

tag: treatment


title: Col0_23C_A

tag: tissue

value: seedlings


title: Col0_29C_B

tag: developmental stage


title: SA03907


title: sample_1

description:
sample-0
C-vs-S_results.txt
C vs S raw.txt


title: Col0_23C_B


title: SA03912


title: control_3

description:
control-2
C-vs-S_results.txt
C vs S raw.txt

source_name: planktonic growth

value: control


title: BA00063: S13-6261

tag: tumor grage

tag: breast cancer stage


title: BA00060: S11-3206


title: SA03879

tag: disease state

tag: batch


title: SA03886


title: control_2

description:
control-1
C-vs-S_results.txt
C vs S raw.txt


title: BA00649: MT1260-083-112

value: RD


title: SA03843


title: BA00019: S09-5100

value: P


title: SA03815


title: control_1

description:
control-0
C-vs-S_results.txt
C vs S raw.txt


title: BA00646: MT1260-083-109


title: S16_planaria + RCTR3 (R-4)

city: Boston

last: Chiang

state: MA

address: 60 Fenwood Rd. 3016Q

department: Anesthesiology

institute: Brigham and Women's Hospital

data_processing:
All coding sequences were translated into peptide sequences using genome-wide functional annotation obtained via orthology assignment by eggNOG-mapper
In order to perform logarithmic transformation, we impute the zero TPM (Transcripts Per Kilobase Million) to the half of minimum TPM.
Wald test was performed using the R package sleuth, which is for differential analysis that leverage the bootstrap estimates of kallisto
The following pathway databases were used: Canonical pathways (CP) and Gene Ontology (GO)
The mean-rank gene set test was used to perform pathway analysis, which tells us if a set of genes tends to be more highly ranked in terms of the Z-scores.
Genome_build: raw_trinity_assembly.fasta and filtered_trinity_cds.fasta files in PMID: 27909700
Supplementary_files_format_and_content: log2 TPM

organism: Dugesia japonica

source_name: planaria + RCTR3

growth_protocol: Planaria (Dugesia japonica; Dj) were kept in water (Poland Spring) at 20°C and starved for 7 days before surgery

extract_protocol:
Total RNA were extracted using Trizol reagent, Poly A+ RNA was enriched.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Head resection was performed (post-ocular surgical injury), and posterior portions were then placed in water together with MCTR3, PCTR3, RCTR3 (10 nM) or vehicle (0.1% ethanol v/v in water).

value: posterior portion after head resection


title: low grade diffuse glioma_7

city: tianjin

first: chang

last: shu

address: 94 weijin road

institute: Tianjin HuanHu hospital,School of medicine,Nankai university

description: Gene expression analysis.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) 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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: frozen tumor tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug 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.

extract_protocol: Only samples with more than 80% tumor cells were selected for RNA extraction. Total RNA from frozen tumor samples was extracted using the mirVana miRNA Isolation kit (Ambion) according to the manufacturer’s protocol. RNA concentration and quality were measured using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). And quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: brain

tag: gender

value: female

tag: grade

value: low grade diffuse glioma


title: low grade diffuse glioma_6

description: Gene expression analysis.

value: male


title: low grade diffuse glioma_3

description: Gene expression analysis.


title: low grade diffuse glioma_5

description: Gene expression analysis.


title: S14_planaria + RCTR3 (R-2)


title: S15_planaria + RCTR3 (R-3)


title: SA03786

city: Los Angeles


title: BA00641: MT1260-083-104

value: N

value: breast cancer


title: S13_planaria + RCTR3 (R-1)


title: low grade diffuse glioma_4

description: Gene expression analysis.


title: SA03792


title: SA03800


title: BA00603: CS15-13818

value: pCR


title: BA00123: HS16-21247(A1)


title: BA00637: MT1260-081-002


title: SA03776


title: BA00536: MT1260-083-98


title: S10_planaria + PCTR3 (P-2)

source_name: planaria + PCTR3


title: S11_planaria + PCTR3 (P-3)


title: SA03765


title: SA03771


title: BA00533: MT1260-083-95


title: low grade diffuse glioma_1

description: Gene expression analysis.


title: high grade diffuse glioma_6

description: Gene expression analysis.

value: high grade diffuse glioma


title: S12_planaria + PCTR3 (P-4)


title: high grade diffuse glioma_7

description: Gene expression analysis.


title: low grade diffuse glioma_2

description: Gene expression analysis.


title: high grade diffuse glioma_4

description: Gene expression analysis.


title: high grade diffuse glioma_5

description: Gene expression analysis.


title: S9_planaria + PCTR3 (P-1)


title: SA03751

value: ARMB


title: SA03739

value: APMB


title: BA00521: MT1260-083-83


title: S8_planaria + MCTR3 (M-4)

source_name: planaria + MCTR3


title: BA00513: MT1260-083-75


title: S7_planaria + MCTR3 (M-3)


title: SA03736

source_name: Peripheral blood


title: YKR1895_H3_IAA_4

city: Planegg-Martinsried

first: Martina

last: Peritore

state: Bayern

address: Am Klopferspitz 18

country: Germany

institute: MPIB

data_processing:
Sequecing reads were mapped to the S. cerevisiae genome using Bowtie2  (version 2.2.9) with default parameters
Multiple mapping reads were filtered with SAMtools.
Genome_build: LYZE00000000.1, sacCer3
Supplementary_files_format_and_content: All files were generated with R. Bed files contain aligned reads, bedGraph files represent read coverage

organism: Saccharomyces cerevisiae

source_name: Cells

growth_protocol: Cells were grown in YP-media containing 2% raffinose at 30°C. Exponentially  growing cells (OD600 0.5-0.7) were synchronized in M phase with 5 μg/ml  nocodazole for 2-3 hours. Cell cycle arrest was assessed via microscopy and  DNA content measured by flow cytometry.

extract_protocol:
Cells were mechanically lysed and chromatin was sheared by sonication to  fragments of 200-500 bp. 40% of the chromatin extract was used for  immunoprecipitation, the purified complexes were treated with proteinase K and crosslinks reversed. DNA was purified by phenol-chloroform extraction and ethanol  precipitation.
Strand-specific ChIP-seq libraries were prepared starting from 1-3 ng of DNA using Accel-NGS® 1S Plus Library Kit following manufacturer instructions and 10-12 cycles were used for library amplification. Clean-up steps were performed with SPRIselect beads.

treatment_protocol: Site-specific DSBs were introduced  inducing the HO endonuclease or the AsiSI restriction enzyme via the galactose  promoter, adding galactose to the cultures to a final concentration of 2%. Cells  were crosslinked at the indicated time points with 1% formaldehyde for 16  minutes at room temperature and the reaction quenched with glycine (final concentration 400 mM). Cells were harvested by centrifugation (3500xg at  4°C), washed with cold PBS and the pellet flash frozen in liquid nitrogen.

tag: chip antibody

value: anti-H3 antibody (RRID:AB_2687473)

tag: genome used for alignment


title: SA03734

last: Chang

address: 10833 Le Conte Ave

institute: University of California, Los Angeles

extract_protocol:
Genomic DNA was extracted from whole blood samples using QIAGEN’s QIAamp DNA Blood Midi/Maxi Kit, performed at Duke. The purified genomic DNA was shipped on ice to University of California, Los Angeles (UCLA) for RRBS library preparation. Genomic DNA was first quantified by Qubit dsDNA BR Assay Kit (ThermoFisher cat. Q32850). The RRBS libraries were prepared as described(52) with the following conditions. For each sample, 100 ng of purified genomic DNA was digested with 20 U of MspI (NEB, cat # R0106L) at 37°C o/n in the presence of RNase Cocktail Mix (Ambion, cat # AM2286). End-repair and adenylation tailing were performed by the addition of Klenow Fragment 3ʹ->5ʹ exo- (NEB, cat # M0212L) in the presence of dATP, dGTP, and d5meCTP (Fermentas). Adapter Ligation was performed by the addition of 0.3 µl of Illumina TruSeq methylated Adapters (Illumina, TruSeq Nano cat# FC-121-4001) and 1 µl of Quick T4 DNA Ligase (NEB cat# M2200L). Samples were pooled and purified using an equal volume of SPRI beads (Beckman Coulter, cat # B23318). Size-selection was performed using SPRI beads to enrich for fragments from 200 to 400 bp. Bisulfite treatment was performed using EpiTect Bisulfite kit (QIAGEN, cat # 59104) according to manufacturer’s protocol, except that two consecutive rounds of conversion were performed, for a total of 10 hr of incubation. Purified converted DNA was PCR amplified using MyTaq HS Mix (Bioline, cat# BIO-25045) and TruSeq PCR Primer Cocktail (Illumina, TruSeq Nano cat# FC-121-4001) according to the following protocol: initial denaturation at 98°C for 30 s; 12 cycles of 98°C for 15 s, 60°C for 30 s, 72°C for 30 s; final extension at 72°C for 5 min. Amplified libraries were purified twice with an equal amount of SPRI beads to remove primer and adapter dimers.
The sequencing data were first demultiplexed based on the barcodes of each sample pooled in the lanes. The data were subjected to a quality control step using FastQC (version 0.11.7), where the low quality reads were discarded from further analysis based on the per base sequence quality and per sequence quality score using the default criteria setting in FastQC(53). Sequencing data were trimmed to remove the adaptors and the terminal CG using the trimmomatic software (v0.38) (54). The reads were aligned to the human genome GRCh38/hg38 (release 93, downloaded from Ensembl) and DNA methylation levels were determined using the BS-Seeker2 pipeline(55) with the aligner bowtie (v1.2.2) and the default settings for the fragment length (20 for lower bound, 500 for upper bound). Samples with less than 5 M total raw reads (3 samples) were excluded from further analyses. On average each sample generated about 36 M total raw reads with 73.7% mappability. Within the study, sequencing data were generated from two sequencing runs, termed batch.


title: BA00528: MT1260-083-90

tag: age


title: S5_planaria + MCTR3 (M-1)


title: YKR1895_H3_IAA_2

tag: strain


title: S6_planaria + MCTR3 (M-2)


title: SA03727


title: SA03716


title: BA00453: MT1260-083-067

tag: response to nac


title: high grade diffuse glioma_3

description: Gene expression analysis.


title: high grade diffuse glioma_2

description: Gene expression analysis.


title: high grade diffuse glioma_1

description: Gene expression analysis.


title: BA00233: MT1260-083-039

tag: estrogen receptor status


title: S3_planaria + vehicle (V-3)

source_name: planaria + vehicle

value: vehicle


title: YKR1895_H3_IAA_6


title: YKR1895_H3_IAA_0


title: BA00230: MT1260-083-036

tag: progesterone receptor status


title: YKR1895_H3_CTR_6


title: SA03712


title: S2_planaria + vehicle (V-2)


title: SA03703


title: YKR1895_H3_CTR_4


title: SA03695


title: YKR1895_H3_CTR_2


title: BA00150: MT-1260-083-019

tag: her2 receptor status


title: YKR1895_H3_CTR_0


title: BA00114: WT169912766(A1)


title: YKR1894_H3_IAA_6


title: SA03618


title: SA03635


title: S4_planaria + vehicle (V-4)

tag: treatment


title: BA00113: HS16-16742(B)

tag: tissue


title: CRC 347 RHAMM- CD44+

city: Fukuoka

first: Michitaka

last: Nakano

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Medicine and Biosystemic Sciences

country: Japan

institute: Kyushu University

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91)  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary human colorectal cancer

growth_protocol: 5000-10000 numbers of cells from freshly isolated colorectal cancer tissues were directly sorted into RNA extraction dilution  by FACS.

extract_protocol: Total RNA was extracted using Trizol (Thermo Fisher Scientific; catalog # 15596026), in accordance with the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: colorectal cancer

tag: patient id

tag: cell markers

value: RHAMM- CD44+


title: YKR1894_H3_IAA_4


title: BA00109: WT169905895(A1)

city: San Diego

last: Chen

address: 4949 Carroll Canyon Road, Suit 120

institute: Certis Oncology Solution

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Raw fastq files from sequencing runs were processed as follows: Atropos was used to remove the adapter sequences from all the reads; STAR aligner was used to map the reads to the human hg38 genome; RSEM was used to quantitate the reads for each individual gene. Finally, the TPM values were used to represent the mRNA expression of each individual genes.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted from FFPE samples and quantified using Qubit4 system.
RNA-seq library preparation was performed according to the AmpliSeq for Illumina Transcriptome Human Gene Expression Panel workflow. Library quality control analysis was performed on the Agilent TapeStation System.  Sample libraries passing TapeStation QC were quantified using the Qubit 4 and then normalized, pooled, and loaded into the Illumina NextSeq 500/550 High output 300 cycle v2.5 kit for sequencing of 2x150 paired-end RNA-Seq.

tag: tumor grage

tag: breast cancer stage


title: SA03596

first: Yu-Ling

tag: disease state

tag: batch


title: BA00225: MT1260-083-031

source_name: MT group breast cancer patients


title: YKR1894_H3_IAA_2


title: CRC 351 RHAMM+ CD44+

value: RHAMM+ CD44+


title: SA03556


title: BA00108: WT169906780(A1)

value: RD

value: P


title: CRC 347 RHAMM+ CD44+


title: SA03660


title: S1_planaria + vehicle (V-1)

value: posterior portion after head resection


title: BA00149: MT-1260-083-018


title: SA03527


title: YKR1894_H3_IAA_0


title: CRC 346 RHAMM- CD44+


title: BA00605: CS15-15702


title: YKR1894_H3_CTR_6


title: CRC 351 RHAMM- CD44+


title: BA00593: CS15-23940


title: YKR1894_H3_CTR_2


title: CRC 346 RHAMM+ CD44+


title: SA03456


title: BA00585: CH17-2006


title: SA03436


title: SA03443


title: YKR1894_H3_CTR_0


title: SA03515


title: BA00604: CS15-17881


title: SA03429


title: HO_asy_H3_4h_II


title: HO_asy_H3_2h_II


title: SA03423


title: BA00568: CS16-10701


title: YKR1894_H3_CTR_4


title: HO_asy_H3_0h_II


title: SA05915


title: cSCC_020

city: Shanghai

first: Sibo

last: Zhu

state: China

address: songhulu 2005

institute: Fudan University

data_processing:
HiSeq 2500 instrument (Illumina) and single-end 50-bp read flow cells were used in this study
Sequenced reads were trimmed for adaptor sequence by trimmomatic(v0.36), then mapped to human genome(hg19) by Hisat2(V2.0.5), and counted by featureCounts(v1.5.2)
data was filterd under the standization that a gene expressed at least in 3 cells and a cells must express at leat 200 features
Genome_build: mm9
Supplementary_files_format_and_content: csv files include count values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: skin

growth_protocol: Eight female Hairless SKH-1 mice aged 7 months were provided by Shanghai SIGMA High-tech Co., Ltd.

extract_protocol:
A piece of skin tissue was cut from each mouse in the WO group  (NC-1, NC-2, NC-3, NC-4). One normal tissue and three skin lesion tissues were cut from each mouse in the UVR group, and four tissues were divided into groups according to the diagnostic criteria for skin squamous cell carcinoma (NC, AK-1, AK-2, cSCC). The RNAs were extracted using TRIZOL reagent (Sigma, USA).
CDNA libraries were prepared by Nextera sample preparation kit (Illumina, USA) according to the instructions. Fragments of 300-450bp length were recovered using Ampure XP Beads (Beckman Coulter, USA). All libraries were quantified using 2100 Bioanalyzer and pooled as 1:1 at 2nM for sequencing in HiSeq 150 pair-end reads (Illumina, USA).

treatment_protocol: The mice were randomly divided into 2 groups of 4 mice each: the without light burn group (WO) and the light burn group (UVR). The UVR group was irradiated with ultraviolet rays every day.

value: Hairless SKH-1 mice

value: skin

value: squamous cell carcinoma (cSCC)


title: Macrophages stimulated with IFN-alpha

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

institute: Graduate School of Medical Sciences, Kumamoto University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: macrophage, IFN-alpha

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Cells were cultured with 10%FBS/RPMI.

extract_protocol: The total RNA was isolated from cells using ReliaPrep TM  RNA Cell Miniprep System (Promega) according to the manufacturer's instructions.

treatment_protocol: Cells were cultured with IFN-alpha or IL-10 (10ng/mL) for 24 hours.

tag: cell type

value: macrophages


title: cSCC_021


title: Unstimulated macrophages

source_name: macrophage, unstimulated


title: cSCC_019


title: HO_asy_RPA_4h_II

tag: chip antibody

value: anti-RFA antibody (Cat# AS07-214, Agrisera)


title: Macrophages stimulated with IL-10

source_name: macrophage, IL-10


title: BA00116: WT169912674(A1)

first: Joan

source_name: breast cancer patients from Hartford Hospital

value: pCR

value: N

value: breast cancer


title: BA00153: S05-1073

source_name: breast cancer patients from UConn Health


title: BR.g8

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Raw data obtained from the Illumina NextSeq 500 was trimmed and aligned as described in Yuan et al, Genome Medicine, 2018. For each read with a unique, strand specific alignment to exonic sequence, we constructed an address comprised of the sample barcode, unique molecular identifier (UMI) barcode, and gene identifier. The resulting address file only contained the addresses from reads with corresponding single index. We generated a digital gene expression matrix and filter sample barcodes as described previously (Yuan et al. 2018). Briefly, reads with the same sample barcode, UMI and aligned gene were collapsed and sequencing errors in the sample barcode and UMI were corrected to generate a  matrix of molecular counts for each cell.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file that contains the gene expression counts of each sample.

source_name: FAC-sorted pDCs from Donor 2

growth_protocol: PBMCs from donors' blood were isoalted by Ficoll gradient (GE Healthcare). pDCs and pan-DCs wre enriched from PBMCs by negative selection using EasySep Human Plasmacytoid DC Enrichment Kit and EasySep Human pan-DC Pre-Enrichment Kit (STEM CELL Technologies) with ~80-90% purity and cultured in RPMI-1640 complete medium with 2 mM L-gluatamine, 1 mM sodium pyruvate, 1x MEM non-essential amino acids, 100 U/mL penicillin-streptomycin, and 10% fetal bovine serum. MRC5 human lung fibroblasts were cultured under the same conditions. All cells were incubated at 37C with 5% carbon dioxide.

extract_protocol:
pDCs were detached from plates by gentle pipetting and stained for viability with the Zombie Aqua Fixable Vaiability Kit in PBS for 20 mins at 4C. Cells were washed in 4C medium and FAC-sorted to remove MRC5 cells based on forward and side-scatter using an SH800Z sorter (SONY Biotechnology). Total RNA from sorted live pDCs was isolated using an RNeasy Mini Kit (QIAGEN).
Pooled RNA-seq was performed using the low-input RNA-seq protocol reported in Snyder et al, Science Immunology, 2019. All of the steps prior below that  come before the barcoded cDNA libraries are pooled were performed using a BioMek  4000 automated liquid handling robot (Beckman). Briefly, we added deoxyribonucleotides  (dNTPs) (ThermoFisher) to a final concentration of 2 mM and reverse transcriptase primer  to 2 uM followed by primer annealing at 72C for 3 mins. We then added 7.5 uL of reverse  transcription mixture to each well comprised of 2M betaine (Affymetrix), 2x ProtoScript  Buffer (NEB), 12 mM MgCl2 (ThermoFisher), 10 mM dithiothreitol (ThermoFisher), 5.3 U  of Protoscript II reverse transcriptase (NEB), 0.53 U of SUPERaseIN (ThermoFisher), and  2 uM template-switching oligo. The reverse transcription reaction was incubated at 42C  for 90 mins followed by 10 cycles of 50C for 2 mins, 42C for 2 mins, and 70C for 10 mins.  Next, 2 uL of exonuclease I (ThermoFisher) was added to each well (1.875 U of  exonuclease I in water) and the resulting mixture was incubated at 37C for 30 mins, 85C  for 15 mins, and 75C for 30s.

treatment_protocol: Cells were stimulated or co-cultured with 2.5 uM CpG, IL-3, 10 MOI CMV, MRC5 cells, or CMV-infected MRC5 cells for 2, 4, 8, 16, or 32 hours.

tag: donor number

value: Donor 2

value: pDCs

value: CMV-infected MRC5 cells

tag: time

value: 32 hr


title: SA05867

value: APMB


title: BR.g9

source_name: FAC-sorted pDCs from Donor 3

value: Donor 3


title: BA00111: WT169901238(A1)

tag: age


title: SA05820


title: BR.g7

source_name: FAC-sorted pDCs from Donor 1

value: Donor 1


title: ATN1-post coculture

description: SAMPLE 2

source_name: ATN1-post coculture

treatment_protocol: Cells were cultured with human monocyte-derived macrophages for 3 weeks.

tag: cell line

value: ATN-1 cell

tag: co-cultured with

value: human monocyte-derived macrophages for 3 wks


title: SA05731


title: HO_asy_RPA_0h_II

tag: strain

tag: genome used for alignment


title: cSCC_018

value: Hairless SKH-1 mice


title: BR.g6

tag: treatment

value: uninfected MRC5 cells


title: HO_asy_RPA_2h_II


title: HO_asy_IN_4h_II


title: SA05712

value: ARMB


title: AK_016

tag: tissue

value: skin

value: actinic keratoses (AK)


title: BR.g5


title: HO_asy_IN_2h_II


title: SA05709


title: AK_015


title: ATN1

description: SAMPLE 1

value: none (mono-culture)


title: AK_014


title: HO_asy_H3_4h_I

value: anti-H3 antibody (RRID:AB_2687473)


title: BR.g3

value: CpG (2.5 uM)


title: SA05567


title: SA05526


title: BR.g2

value: Donor 2


title: SA05525


title: AK_013


title: HO_asy_H3_2h_I


title: AK_017


title: SA05315


title: AK_012


title: AK_011


title: SA05500


title: BR.f8

value: pDCs

value: 16 hr


title: AK_010


title: BR.g1

value: 32 hr


title: HO_asy_RPA_2h_I

value: anti-RFA antibody (Cat# AS07-214, Agrisera)


title: BR.f9

value: Donor 3

value: CMV-infected MRC5 cells


title: BR.g4

value: Donor 1


title: BR.f7


title: NS_009

value: normal skin (NS)


title: SA05300


title: HO_asy_IN_0h_II


title: SA05272

value: APMB


title: NS_008

value: Hairless SKH-1 mice


title: BR.f6

value: uninfected MRC5 cells


title: HO_asy_IN_4h_I


title: SA05238


title: NS_007

value: skin


title: HO_asy_IN_2h_I


title: HO_asy_H3_0h_I


title: SA05208


title: NS_006


title: HO_asy_RPA_4h_I


title: BR.f5


title: HO_asy_IN_0h_I


title: BA00532: MT1260-083-94

tag: response to nac

value: RD

tag: estrogen receptor status

value: N

tag: progesterone receptor status

tag: her2 receptor status

value: breast cancer


title: BR.f4


title: SA05170

tag: disease state

value: ARMB


title: BR.f3

value: CpG (2.5 uM)


title: BR.f2

value: Donor 2

value: pDCs


title: SA05121

tag: batch


title: H3_6_MNase2

value: anti-H3 antibody (RRID:AB_2687473)


title: SA05101


title: NS_004


title: NS_005


title: H3_4_MNase2


title: HO_asy_RPA_0h_I

value: anti-RFA antibody (Cat# AS07-214, Agrisera)


title: H3_2_MNase2


title: SA05073


title: NS_002


title: NS_001


title: H3_0_MNase2


title: BR.f1

tag: cell type

value: 16 hr


title: SA05051


title: SA05030


title: WT-2 RA 24 h H3K4me3 chip-seq

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of 4C were mapped to mm10 with pipe4C. Then we obtained the wig
Clean reads of ChIP-seq were mapped to mm10 using Bowtie2(2.3.1)
peaks were called using deeptools-bamCompare(3.1.3) .
Genome_build: mm10
Supplementary_files_format_and_content: Text files include genes counts values,ChIP and 4C signal peaks for each Sample

source_name: Embryonic stem cells

growth_protocol: Mouse ESCs were grown in culture dishes coated with 0.1% gelatin in Glasgow Minimum Essential Medium (GMEM) supplemented with 15% fetal bovine serum (FBS), 100 nM nonessential amino acids, 1 % sodium pyruvate, 200 mM glutamate, 1% penicillin-streptomycin, 50 uM β-mercaptoethanol, 10 ng/mL LIF, 1uM PD0325901 (a MEK inhibitor) and 3 uM CHIR99021 (a GSK inhibitor). The medium was replaced every 2-3 days

extract_protocol:
For RNA -seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions; For 4C-seq: cells were treated with DpnII and NlaIII as the first and second restriction enzymes, respectively. The primers were used to amplify the final 4C template for generating 4C-seq libraries and DNA was extracted according to the manufacturer's instructions; For ChIP-seq: cells were cross-linked with 1% formaldehyde. Sonication was carried out to shear the chromatin to yield DNA fragment sizes of 100 to 500 base pairs (bp). Samples were cleared and precleared for 1 hour with 40 μl of protein A/G agarose beads. Part of the precleared samples was used as input, and the remainder was immunoprecipitated with H3K27ac and H3K4me3 antibody and protein A/G agarose beads. The precipitated DNA and input DNA were sequenced using an Illumina sequencer. Reads were mapped to the mm10 reference genome using HISAT2 and further analyzed with HOMER package.
RNA, ChIP-seq and 4C libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RA treatment, ESCs were induced to differentiate by LIF/2i withdrawal and addition of 2 uM RA (Sigma). Culture medium was replaced every day.

value: ESC cell line E14

value: embryo, blastocyst embryo, blastocyst

value: RA induced differentiation 1 day

tag: genotype

tag: chip antibody


title: WT-1 RA 24 h H3K4me3 chip-seq


title: BR.e10

tag: donor number

value: Donor 1

value: IL3 + CMV (10 MOI)

tag: time

value: 8 hr


title: SA05019

data_processing:
Read quality was checked using FastQC (version 0.11.7)
Reads with the adaptors and the terminal CG were trimmed using the trimmomatic software (v0.38)
Reads aligned using BS-Seeker2 pipeline with the aligner bowtie (v1.2.2)
Genome_build: cohort1(Hg19); cohort2(Hg38)
Supplementary_files_format_and_content: [CGfinal files] chromosome, dinucleotide, position, methylated counts, total counts, methylation frequency, 95% confidence interval for methylation frequency

value: APMB


title: H3_4_MNase1


title: WT-2 RA 24 h H3K27ac chip-seq

tag: cell line


title: BR.e9

value: Donor 3


title: SA05004


title: BR.e8


title: BR.e11


title: BR.e7


title: BR.e12


title: H3_0_MNase1


title: WT-1 RA 24 h H3K27ac chip-seq


title: 2-3 WT 4C-Rep1

data_processing:
Library strategy: 4C
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with HTSeq (0.9.1)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of 4C were mapped to mm10 with pipe4C. Then we obtained the wig
Clean reads of ChIP-seq were mapped to mm10 using Bowtie2(2.3.1)
peaks were called using deeptools-bamCompare(3.1.3) .
Genome_build: mm10
Supplementary_files_format_and_content: Text files include genes counts values,ChIP and 4C signal peaks for each Sample


title: H3_2_MNase1


title: SA04942


title: 2-1 WT 4C-Rep2


title: IN_H3flag_1_8_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:8
IN_43_1:8_I_AGGCGAAGAGCGATAG

value: anti-FLAG beads (RRID:AB_2637089)


title: SA04908


title: IN_H3flag_1_8_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:8
IN_43_1:8_II_GTACTGACGAGATTCC


title: 2-3 WT 4C-Rep2


title: BR.e5

value: free CMV (10 MOI)


title: IN_H3flag_1_8_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:8
IN_43_1:8_CCTATCCTTAATGCGC


title: SA04886


title: SA04915


title: BR.e6


title: H3_6_MNase1


title: 2-1 WT 4C-Rep1


title: SA04878

value: ARMB


title: IN_H3flag_1_6_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:6
IN_43_1:6_I_AGGCGAAGTCTCGCGC


title: BR.e3


title: 1-1 WT 4C-Rep2


title: SA04873


title: BR.e2


title: 1-1 WT 4C-Rep1


title: IN_H3flag_1_6_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:6
IN_43_1:6_CCTATCCTCTGAAGCT


title: SA04864


title: D-KO-RNA-seq-Rep3

value: D-KO


title: SA04862


title: IN_H3flag_1_4_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:4
IN_43_1:4_I_AGGCGAAGTCCGCGAA


title: SA04821


title: BR.e1


title: SA04859


title: D-KO-RNA-seq-Rep2


title: E2-KO-RNA-seq-Rep3


title: IN_H3flag_1_2_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:2
IN_43_1:2_II_GTACTGACATTACTCG


title: IN_H3flag_1_4_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:4
IN_43_1:4_CCTATCCTGAATTCGT


title: D-KO-RNA-seq-Rep1


title: BR.d8

value: Donor 2

value: CMV-infected MRC5 cells


title: BR.d9

value: pDCs


title: E2-KO-RNA-seq-Rep2


title: BR.d7


title: SA04816


title: IN_H3flag_1_2_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:2
IN_43_1:2_I_AGGCGAAGCGGCTATG


title: BR.d6

value: uninfected MRC5 cells


title: BR.e4


title: IN_H3flag_1_6_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:6
IN_43_1:6_II_GTACTGACCGCTCATT


title: SA04785


title: IN_H3flag_1_4_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:4
IN_43_1:4_II_GTACTGACTCCGGAGA


title: E2-KO-RNA-seq-Rep1


title: BR.d5


title: IN_H3flag_1_2_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:2
IN_43_1:2_CCTATCCTATTCAGAA


title: SA04782


title: E1-KO-RNA-seq-Rep3


title: BR.d4


title: SA04751


title: IN_H3flag_1_1_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:1
IN_43_1:1_II_CAGGACGTAGCGATAG


title: E1-KO-RNA-seq-Rep2


title: SA04742


title: SA04721


title: IN_H3flag_1_1_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:1
IN_43_1:1_CCTATCCTGAGATTCC


title: BR.d2

value: CpG (2.5 uM)


title: IN_H3flag_1_0_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:0
IN_43_10h_II_GTACTGACATTCAGAA


title: IN_H3flag_1_1_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:1
IN_43_1:1_I_AGGCGAAGTAATGCGC


title: BR.d1


title: SA04711


title: SA04633


title: E1-KO-RNA-seq-Rep1

value: ESC cell line E14


title: BR.c11

value: 4 hr


title: IN_H3flag_1_0_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:0
IN_43_10h_CCTATCCTCGGCTATG


title: IN_H3flag_1_0_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:0
IN_43_10h_I_TAATCTTAATTACTCG


title: WT-RNA-seq-Rep2

value: embryo, blastocyst embryo, blastocyst

value: RA induced differentiation 1 day

value: WT


title: IN_H3flag_0_1_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 0:1
IN_43_0h_II_CAGGACGTTCTCGCGC


title: BR.c12

value: IL3 + CMV (10 MOI)


title: SA04627

value: APMB


title: BR.c10

value: Donor 1


title: SA04547


title: BR.c9

value: Donor 3


title: IN_H3flag_0_1_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 0:1
IN_43_0h_I_AGGCGAAGCTGAAGCT

value: anti-FLAG beads (RRID:AB_2637089)


title: BR.d3

value: 8 hr


title: SA04535

value: ARMB


title: IN_H3flag_0_1_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 0:1
IN_43_0h_CCTATCCTCGCTCATT


title: SA04529


title: BR.c7


title: WT-RNA-seq-Rep3


title: IN_ctr_1_8_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:8
IN_517_1:8_II_CAGGACGTCGGCTATG


title: SA04497


title: BR.c6

value: free CMV (10 MOI)


title: SA04471


title: SA04495


title: BR.c5

value: Donor 2


title: IN_ctr_1_8_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:8
IN_517_1:8_CCTATCCTATTACTCG


title: BR.c4

value: pDCs


title: IN_ctr_1_6_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:6
IN_517_1:6_II_CAGGACGTTAATGCGC


title: WT-RNA-seq-Rep1


title: SA04469


title: IN_ctr_1_6_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:6
IN_517_1:6_ATAGAGGCAGCGATAG


title: BR.c2


title: SA04413


title: BR.c3


title: BR.c8


title: IN_ctr_1_4_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:4
IN_517_1:4_II_CAGGACGTCTGAAGCT


title: SA04468


title: IN_ctr_1_6_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:6
IN_517_1:6_I_AGGCGAAGGAGATTCC


title: IN_ctr_1_4_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:4
IN_517_1:4_I_AGGCGAAGCGCTCATT


title: BR.c1


title: SA04395


title: BR.b9

value: CMV-infected MRC5 cells


title: BR.b8


title: IN_ctr_1_4_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:4
IN_517_1:4_ATAGAGGCTCTCGCGC


title: BR.b7


title: SA04378


title: IN_ctr_1_2_III

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:2
IN_517_1:2_II_CAGGACGTGAATTCGT


title: SA04329


title: BR.b6

value: uninfected MRC5 cells


title: SA04322


title: IN_ctr_1_2_II

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:2
IN_517_1:2_I_AGGCGAAGTCCGGAGA


title: BR.b5


title: BR.b4


title: IN_ctr_1_2_I

description:
Damaged (6h DSB induction) and undamaged cells mixed 1:2
IN_517_1:2_ATAGAGGCTCCGCGAA


title: SA04256


title: SA04260


title: SA04255