title: Sample 81

status: Public on Mar 18 2018

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

description:
processed data files:
Indels.xls
5'-end trimming of R1: 1 - 5
3-end trimming of R1: 146-150

data_processing:
Library strategy: DNA-seq
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Raw read qualities were evaluated by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ). For paired ended sequencing, only R1 reads were used. Adaptor sequences and read sequences on both ends with Phred quality score lower than 28 were trimmed. Trimmed reads were then mapped with the BWA-MEM algorithm (BWA v0.7.9a) to target sequences. After being piped up with samtools (v0.1.18), indels and base substitutions were further calculated.
Substitution calling was done by SAMtools (version: 0.1.18) mpileup option.  Base substitutions were selected at each position of the examined sgRNA (or crRNA) target sites that mapped with at least 1,000 independent reads, and obvious base substitutions were only observed at the targeted base editing sites. Counts of reads for each base and total reads are listed in individual samplexx_variation.xls. Base substitution frequencies were calculated by dividing base substitution reads by total reads.
Indel calling was calculated from CIGAR values of the SAM/BAM files. For Cpf1, indels were estimated in the aligned regions spanning from upstream 3 nucleotides to the downstream 48 nucleotides both according to PAM sites (55bp). For Cas9, indels were estimated in the aligned regions spanning from upstream eight nucleotides to the target site to downstream 19 nucleotides to PAM sites (50 bp). Indel frequencies were subsequently calculated by dividing reads containing at least one inserted and/or deleted nucleotides by all the mapped reads at the same region. Counts of indel-containing reads and total mapped reads are listed Indels.xls.
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Excel file with Indels (on series record) and text file with Base Subtitutions (on sample records).

source_name: U2OS CDK, DYR, FAN, RUN, S4 NT DNA rep 3

growth_protocol: 293FT and U2OS from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and have been tested for mycoplasma contamination free.

extract_protocol:
For DNA, 72 hr after transfection, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre).
For DNA, DNA-seq libraries were prepared with Illumina TruSeq ChIP Sample Preparation Kit. Deep sequencing was performed on Illumina Hiseq 2500 and Hiseq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: For base editing in genomic DNA, cells were seeded in a 24-well plate at a density of 200,000 per well and transfected with 500 μl serum-free Opti-MEM that contained 5.04 μl LIPOFECTAMINE LTX (Life, Invitrogen), 1.68 μl LIPOFECTAMINE plus (Life, Invitrogen), 1 μg pCMV-dCpf1-BE0 (pCMV-dCpf1-BE, pCMV-dCpf1-BE-YE, pCMV-dCpf1-BE-YEE, pCMV-dCpf1-eBE, pCMV-dCpf1-eBE-YE, pCMV-BE2 or pCMV-BE3), and 0.68 μg crRNA or sgRNA-expressing plasmid. After 72 hr, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre).

tag: type

value: DNA

value: NT


title: Sample 80

type: SRA

description:
processed data files:
Indels.xls
5'-end trimming of R1: 1 - 5
3-end trimming of R1: 121-150

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: U2OS CDK, DYR, FAN, RUN, S4 NT DNA rep 1

tag: cell line

tag: treatment


title: Sample 82

source_name: U2OS CDK, DYR, FAN, RUN, S4 NT DNA rep 2


title: Sample 78

source_name: U2OS CDK, DYR, FAN, RUN, S4 dCpf1-BE DNA rep 3


title: Sample 77

source_name: U2OS CDK, DYR, FAN, RUN, S4 dCpf1-BE DNA rep 2


title: Sample 79

source_name: U2OS CDK, DYR, FAN, RUN, S4 dCpf1-BE DNA rep 1


title: Sample 75

description:
processed data files:
No indel processed data
5'-end trimming of R1: 1 - 5
3-end trimming of R1: 121-150

source_name: CDK_OT3 OT4, DNM_OT3 OT4, DYR_OT3 OT4, EMX_OT3 OT4, FAN_OT3 OT4, RUN_OT3, S3_OT4, S4_OT4 NT DNA rep 3

value: NT off targets


title: Sample 70

source_name: CDK_OT5 OT6, DNM_OT5, DYR_OT5, EMX_OT5, FAN_OT5 OT6, RUN_OT5 OT6, S3_OT5 OT6, S4_OT5 OT6 NT DNA rep 1


title: Sample 74

source_name: CDK_OT1, DNM_OT1 OT2, DYR_OT1 OT2, EMX_OT1 OT2, FAN_OT1, RUN_OT1 OT2, S3_OT1 OT2, S4_OT1 OT2 NT DNA rep 3


title: Sample 71

source_name: CDK_OT1, DNM_OT1 OT2, DYR_OT1 OT2, EMX_OT1 OT2, FAN_OT1, RUN_OT1 OT2, S3_OT1 OT2, S4_OT1 OT2 NT DNA rep 2


title: Sample 76

source_name: CDK_OT5 OT6, DNM_OT5, DYR_OT5, EMX_OT5, FAN_OT5 OT6, RUN_OT5 OT6, S3_OT5 OT6, S4_OT5 OT6 NT DNA rep 3


title: Sample 73

source_name: CDK_OT5 OT6, DNM_OT5, DYR_OT5, EMX_OT5, FAN_OT5 OT6, RUN_OT5 OT6, S3_OT5 OT6, S4_OT5 OT6 NT DNA rep 2


title: Sample 72

source_name: CDK_OT3 OT4, DNM_OT3 OT4, DYR_OT3 OT4, EMX_OT3 OT4, FAN_OT3 OT4, RUN_OT3, S3_OT4, S4_OT4 NT DNA rep 2


title: Sample 67

source_name: CDK_OT5 OT6, DNM_OT5, DYR_OT5, EMX_OT5, FAN_OT5 OT6, RUN_OT5 OT6, S3_OT5 OT6, S4_OT5 OT6 dCpf1-BE DNA rep 3

value: dCpf1-BE off targets


title: Sample 68

source_name: CDK_OT1, DNM_OT1 OT2, DYR_OT1 OT2, EMX_OT1 OT2, FAN_OT1, RUN_OT1 OT2, S3_OT1 OT2, S4_OT1 OT2 NT DNA rep 1


title: Sample 65

source_name: CDK_OT1, DNM_OT1 OT2, DYR_OT1 OT2, EMX_OT1 OT2, FAN_OT1, RUN_OT1 OT2, S3_OT1 OT2, S4_OT1 OT2 dCpf1-BE DNA rep 3


title: Sample 69

source_name: CDK_OT3 OT4, DNM_OT3 OT4, DYR_OT3 OT4, EMX_OT3 OT4, FAN_OT3 OT4, RUN_OT3, S3_OT4, S4_OT4 NT DNA rep 1


title: Sample 64

source_name: CDK_OT5 OT6, DNM_OT5, DYR_OT5, EMX_OT5, FAN_OT5 OT6, RUN_OT5 OT6, S3_OT5 OT6, S4_OT5 OT6 dCpf1-BE DNA rep 2


title: TDP-43-silenced SK-N-BE cells, biological rep 2 (exon-level)

type: RNA

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

molecule: total RNA

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: The human neuroblastoma SK-N-BE cell line was cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1mM sodium pyruvate, 2 mM l-glutamine, 4.5 g/l glucose and 100units/ml penicillin and 100g/ml streptomycin.

extract_protocol: Total RNA was isolated using the RNeasy Plus Mini kit (Qiagen) from TDP-43, FUS or control mock siRNA-treated SK-N-BE cells.

treatment_protocol: For gene silencing of TDP-43 and FUS RBPs, SK-N-BE cells were transfected for 96 hours with 80nM of specific siRNA duplexes (Darmakon and Invitrogen, respectively) in a double round of transfection using Lipofectamine 2000 (Invitrogen). Stealth siRNA low GC (Invitrogen) was used as a negative control.

value: neuroblastoma SK-N-BE

value: 96-hour TDP-43 gene silencing


title: Sample 63

source_name: CDK_OT3 OT4, DNM_OT3 OT4, DYR_OT3 OT4, EMX_OT3 OT4, FAN_OT3 OT4, RUN_OT3, S3_OT4, S4_OT4 dCpf1-BE DNA rep 2


title: TDP-43-silenced SK-N-BE cells, biological rep 1 (exon-level))


title: Sample 62

source_name: CDK_OT1, DNM_OT1 OT2, DYR_OT1 OT2, EMX_OT1 OT2, FAN_OT1, RUN_OT1 OT2, S3_OT1 OT2, S4_OT1 OT2 dCpf1-BE DNA rep 2


title: TDP-43-silenced SK-N-BE cells, biological rep 3 (exon-level)


title: control-silenced SK-N-BE cells, biological rep 3 (exon-level)

source_name: siCTRL

value: 96-hour Control gene silencing


title: FUS-silenced SK-N-BE cells, biological rep 3 (exon-level)

source_name: siFUS

value: 96-hour FUS gene silencing


title: control-silenced SK-N-BE cells, biological rep 1 (exon-level)


title: Sample 59

source_name: CDK_OT1, DNM_OT1 OT2, DYR_OT1 OT2, EMX_OT1 OT2, FAN_OT1, RUN_OT1 OT2, S3_OT1 OT2, S4_OT1 OT2 dCpf1-BE DNA rep 1


title: FUS-silenced SK-N-BE cells, biological rep 2 (exon-level)


title: Sample 56

description:
processed data files:
Indels.xls
5'-end trimming of R1: 1 - 5
3-end trimming of R1: 101-150

source_name: CFTR, PD1, S6, VEGFA, RAG1-T, S6-T, VEGFA-T NT DNA rep 2


title: Sample 53

description:
processed data files:
Indels.xls
5'-end trimming of R1: 1 - 5
3-end trimming of R1: 106-150

source_name: FAN NT DNA rep 2 and CDK, DNM, DYR, S4, S3 NT DNA rep 3


title: Sample 52

description:
processed data files:
Indels.xls
5'-end trimming of R1: 1 - 5
3-end trimming of R1: 116-150

source_name: CDK, DNM, DYR, FAN, S4, S3 NT DNA rep 1 and RUN, EMX NT DNA rep2


title: Sample 51

description:
processed data files:
Indels.xls
5'-end trimming of R1: 1 - 5
3-end trimming of R1: 126-150

source_name: RUN, EMX NT DNA rep 1


title: Sample 57

source_name: CFTR, PD1, S6, VEGFA, RAG1-T, S6-T, VEGFA-T NT DNA rep 3


title: Sample 58

source_name: CFTR, PD1, S6, VEGFA, RAG1-T, S6-T, VEGFA-T NT DNA rep 1


title: Sample 66

source_name: CDK_OT3 OT4, DNM_OT3 OT4, DYR_OT3 OT4, EMX_OT3 OT4, FAN_OT3 OT4, RUN_OT3, S3_OT4, S4_OT4 dCpf1-BE DNA rep 3


title: control-silenced SK-N-BE cells, biological rep 2 (exon-level)


title: FUS-silenced SK-N-BE cells, biological rep 1 (exon-level)


title: Sample 50

source_name: FAN dCpf1-eBE-YE DNA rep 1


title: Sample 60

source_name: CDK_OT3 OT4, DNM_OT3 OT4, DYR_OT3 OT4, EMX_OT3 OT4, FAN_OT3 OT4, RUN_OT3, S3_OT4, S4_OT4 dCpf1-BE DNA rep 1


title: Sample 55

description:
processed data files:
Indels.xls
5'-end trimming of R1: 1 - 5
3-end trimming of R1: 131-150

source_name: FAN, RUN NT DNA rep 3


title: Sample 48

source_name: DYR, RUN dCpf1-eBE-YE DNA rep 3


title: Sample 61

source_name: CDK_OT5 OT6, DNM_OT5, DYR_OT5, EMX_OT5, EMX_OT5, FAN_OT5 OT6, RUN_OT5 OT6, S3 OT5 OT6, S4_OT5 OT6 dCpf1-BE DNA rep 1


title: Sample 49

source_name: DYR, RUN dCpf1-eBE-YE DNA rep 1 and FAN dCpf1-eBE-YE DNA rep 2


title: WB, Day 44, PID 16

status: Public on Mar 19 2018

city: Rixensart

first: Laurane

last: De Mot

address: Rue de l'Institut 89

country: Belgium

institute: GSK Vaccines

description: WB sample, 14 days after 2nd vaccination

hyb_protocol: After fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on GeneChip_ Human Genome U133 Plus 2.0 arrays following standard procedures.

scan_protocol: Data acquisition was performed using GeneChip Operating Software (Affymetrix).

data_processing: The data were analyzed with R/Bioconductor using GCRMA as summarization/normalization method

source_name: WB samples from subject 16 at Day 44

label_protocol: Biotinylated cDNA were prepared according to NuGen Ovation WB amplification protocol from 50ng total RNA

extract_protocol: Total RNA was isolated by PAXgene Blood RNA kit (Qiagen) according to the manufacturer’s protocol. A DNAse treatment was applied on the PAXgene RNA spin column to avoid genomic DNA contamination. RNA was quantified by UV-spectrophotometry.

treatment_protocol: PAXgene preserved whole blood samples were centrifuged, resuspended in lysis buffer and treated with proteinase K.

tag: tissue

value: Whole Blood (WB)

tag: subject id

tag: sample day


title: Sample 47

source_name: DYR, RUN dCpf1-eBE-YE DNA rep 2 and FAN dCpf1-eBE-YE DNA rep 3


title: Sample 43

source_name: FAN, RUN dCpf1-eBE DNA rep 1


title: Sample 44

source_name: DYR dCpf1-eBE DNA rep 2


title: Sample 41

source_name: CDK, DYR, RUN, S4 dCpf1-BE-YEE DNA rep 3


title: Sample 39

source_name: DYR, FAN, RUN, S4 dCpf1-BE-YEE DNA rep 1


title: Sample 40

source_name: CDK, DYR, RUN, S4 dCpf1-BE-YEE DNA rep 2 and FAN dCpf1-BE-YEE DNA rep 3


title: Sample 36

source_name: RUN, S4 dCpf1-BE-YE DNA rep 2 and CDK, FAN dCpf1-BE-YE DNA rep 3


title: Sample 37

source_name: DYR, S4, RUN dCpf1-BE-YE DNA rep 3


title: Sample 35

source_name: CDK, DYR, FAN dCpf1-BE-YE DNA rep 1


title: Sample 42

source_name: CDK dCpf1-BE-YEE DNA rep 1 and FAN dCpf1-BE-YEE DNA rep 2


title: Sample 38

source_name: RUN, S4 dCpf1-BE-YE DNA rep 1 and CDK, DYR, FAN dCpf1-BE-YE DNA rep 2


title: Sample 46

source_name: DYR  dCpf1-eBE DNA rep 1 and FAN, RUN dCpf1-eBE DNA rep 2


title: Sample 45

source_name: DYR, FAN, RUN dCpf1-eBE DNA rep 3


title: Endometrial_Tissue_RIF_24

city: Istanbul

first: Tuba

last: Günel

address: İstanbul Üniversitesi Fen Fakültesi Moleküler Biyoloji ve Genetik Bölümü Vezneciler

department: Department of Molecular Biology and Genetics

country: Turkey

institute: Istanbul University

description: Gene expression in the endometrium of RIF patient during the window of implantation

hyb_protocol: Fragmented cRNA samples were hybridized onto Agilent Sure Print G3 8x60K Version 2 Microarray slide, by incubation at 65 C for 17 hours with constant rotation. The microarray slides were then washed in two steps of 1 minute in two washing buffers (Agilent Technologies). In order to enhance reproducibility across the different chemical surfaces used, a reference sample was spotted in duplicate on each type of surface to calculate experimental intra- and inter-coefficient of variation and to optimize the array reading parameters (such as laser intensity, focus mass and mass range). The reference sample was taken from a pool (5 μl) of tissue samples (500 μl per patient) from five women with RIF and from five controls without RIF, selected at random.

scan_protocol: The slides were scanned by an Agilent SureScan Microarray Scanner (model G2600D) using one color scan setting for 8x60k array slides.

data_processing: Hybridization signals were extracted using the Agilent Feature Extraction software, version 11.0.1.1. Background correction and quantile normalization was performed using the R package limma.

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 24

label_protocol: First-strand cDNAs were transcribed from 100 ng total RNA with the use of T7-Oligo (dT) Promoter Primers. Samples were transcribed in vitro and Cy-3 labeled, all with the Low Input Quick Amp Labeling kit (Agilent Technologies). The labeling reaction typically yielded 120-200 ng/μl of complementary RNA (cRNA) with a specific activity >10.

extract_protocol: Total RNA were extracted from the endometrium tissues samples; as 24 RIF patients and 24 controls, under cold chain conditions with QIAGEN RNeasy Plus Mini Isolation Kit according to the manufacturer’s instructions. The quantity and quality of obtained total RNA were firstly measured by NanoDrop ND-2000 Spectrophotometer (Thermo Fisher Scientific) and secondly by the Agilent RNA Nano Chip kit on Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA).

value: Endometrial tissue


title: WB, Day 37, PID 6

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 6 at Day 37


title: Endometrial_Tissue_RIF_16

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 16


title: Endometrial_Tissue_RIF_15

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 15


title: Sample 33

source_name: FAN, RUN nCas9-BE3 DNA rep 1 and CDK, DYR nCas9-BE3 DNA rep 2 and DNM, EMX nCas9-BE3 DNA rep 3


title: Sample 34

source_name: S3 nCas9-BE3 DNA rep 2 and RUN, FAN nCas9-BE3 DNA rep 3


title: Sample 32

source_name: FAN, RUN nCas9-BE3 DNA rep 2 and CDK, DYR nCas9-BE3 DNA rep 3


title: Endometrial_Tissue_RIF_14

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 14


title: Endometrial_Tissue_RIF_13

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 13


title: Endometrial_Tissue_RIF_22

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 22


title: Endometrial_Tissue_RIF_20

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 20


title: Endometrial_Tissue_RIF_19

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 19


title: Endometrial_Tissue_RIF_21

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 21


title: Endometrial_Tissue_RIF_18

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 18


title: Sample 31

source_name: CDK, DYR nCas9-BE3 DNA rep 1 and DNM, EMX nCas9-BE3 DNA rep 2, S3 nCas9-BE3 DNA rep 3


title: Sample 29

source_name: CDK, DNM, DYR, FAN, RUN, S3 dCas9-BE2 DNA rep 3


title: Endometrial_Tissue_RIF_23

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 23


title: Endometrial_Tissue_RIF_10

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 10


title: Endometrial_Tissue_RIF_17

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 17


title: Sample 28

source_name: FAN, RUN dCas9-BE2 DNA rep 1 and CDK, S3 dCas9-BE2 DNA rep2


title: Sample 27

source_name: FAN, RUN, DYR dCas9-BE2 DNA rep 2 and EMX dCas9-BE2 DNA rep 3


title: Sample 26

source_name: CDK, DYR, S3 dCas9-BE2 DNA rep 1 and DNM, EMX dCas9-BE2 DNA rep 2


title: Endometrial_Tissue_RIF_12

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 12


title: Sample 30

source_name: DNM, EMX, S3 nCas9-BE3 DNA rep 1


title: Sample 25

source_name: DNM, EMX dCas9-BE2 DNA rep 1


title: Sample 24

description:
Sample 19-24 are the deep-sequeucing mixtures of the treatments by dCpf1-BE0 or dCas9-BE2. Indeed, the experiment was performed separately by either dCpf1-BE0 or dCas9-BE2. They were only mixed before library preparation for sequencing. We mixed different targets together to save barcodes since only small amount of reads for each sample is required.
processed data files:
Indels.xls
5'-end trimming of R1: 1 - 5
3-end trimming of R1: 101-150

source_name: CDK, DNM, DYR, FAN, RUN, S4 dCpf1-BE0- DNA rep c and VEGFA nCas9-BE3 DNA rep 3

value: dCpf1-BE0- or nCas9-BE3


title: Endometrial_Tissue_RIF_9

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 9


title: Sample 23

source_name: CDK, DNM, DYR, FAN, RUN, S4 dCpf1-BE0- DNA rep b and VEGFA nCas9-BE3 DNA rep 2


title: Endometrial_Tissue_RIF_5

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 5


title: Endometrial_Tissue_RIF_6

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 6


title: Sample 20

source_name: CDK, DNM, DYR, FAN, RUN, S4 dCpf1-BE0 DNA rep a and VEGFA dCas9-BE2 DNA rep 1

value: dCpf1-BE0 or dCas9-BE2


title: Sample 22

source_name: CDK, DNM, DYR, FAN, RUN, S4 dCpf1-BE0- DNA rep a and VEGFA nCas9-BE3 DNA rep 1


title: Sample 21

source_name: CDK, DNM, DYR, FAN, RUN, S4 dCpf1-BE0 DNA rep b and VEGFA dCas9-BE2 DNA rep 2


title: Endometrial_Tissue_RIF_8

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 8


title: Endometrial_Tissue_RIF_11

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 11


title: Sample 19

source_name: CDK, DNM, DYR, FAN, RUN, S4 dCpf1-BE0 DNA rep c and VEGFA dCas9-BE2 DNA rep 3


title: Sample 18

source_name: CDK, DNM, DYR, FAN, RUN, S4 dCpf1-BE0 DNA rep 3


title: Endometrial_Tissue_RIF_4

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 4


title: Sample 17

source_name: DNM dCpf1-BE0 DNA rep 1 and CDK, DYR, FAN, RUN dCpf1-BE0 DNA rep 2


title: Sample 14

source_name: S4 dCpf1-BE0 DNA rep 2


title: Sample 15

source_name: S4 dCpf1-BE0 DNA rep 1


title: Sample 16

source_name: CDK, DYR, FAN, RUN dCpf1-BE0 DNA rep 1 and DNM dCpf1-BE0 DNA rep 2


title: Endometrial_Tissue_RIF_1

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 1


title: Endometrial_Tissue_RIF_3

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 3


title: Sample 13

source_name: RAG1-T dCpf1-BE DNA rep 1


title: Endometrial_Tissue_RIF_7

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 7


title: Endometrial_Tissue_Fertile_Control_20

description: Gene expression in the endometrium of fertile control during the window of implantation

source_name: Endometrial Tissue, Control, replicate 20


title: Endometrial_Tissue_Fertile_Control_22

source_name: Endometrial Tissue, Control, replicate 22


title: Endometrial_Tissue_Fertile_Control_21

source_name: Endometrial Tissue, Control, replicate 21


title: Endometrial_Tissue_Fertile_Control_24

source_name: Endometrial Tissue, Control, replicate 24


title: Sample 12

source_name: CFTR, PD1, S6 dCpf1-BE DNA rep 1


title: Endometrial_Tissue_Fertile_Control_23

source_name: Endometrial Tissue, Control, replicate 23


title: Endometrial_Tissue_RIF_2

source_name: Endometrial Tissue, Recurrent Implantation Failure, replicate 2


title: FUS-silenced SK-N-BE cells, biological rep 3 (transcription-level)

source_name: siFUS


title: FUS-silenced SK-N-BE cells, biological rep 2 (transcription-level)


title: Endometrial_Tissue_Fertile_Control_18

source_name: Endometrial Tissue, Control, replicate 18


title: Sample 11

source_name: RAG1-T, S6-T, VEGFA-T dCpf1-BE DNA rep 3


title: Endometrial_Tissue_Fertile_Control_19

source_name: Endometrial Tissue, Control, replicate 19


title: HLA-G+ trophoblast from K113 donor

city: Singapore

first: Cheryl

last: Lee

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were first transformed by variance stabilisation, then normalised using quantile normalisation from lumi

label: Biotin

source_name: Placenta

label_protocol: Good quality final products as assessed by the 2100 Bioanalyzer Instrument were biotinylated using the Encore Biotin Module by NuGEN (#4200-12)

extract_protocol: Cells were lysed in TRIzol and 200 µL of chloroform was added for every 1 mL of TRIzol. The mixture was then vortexed and centrifuged at 8000 RCF, 4°C, for 15 min. The upper aqueous phase was transferred to a new tube, 1.5 times volume of ethanol was added and the entire content was then centrifuged through Purelink™ columns (Invitrogen #12183-016). RNA was purified from the columns following the manufacturer’s protocol, including the DNase step. The final product was eluted in 12 µL of RNase-free water.

tag: donor

tag: trophoblast

value: HLA-G+

tag: gestational age

value: 8 weeks


title: EGFR+ trophoblast from K112 donor

value: EGFR+


title: Endometrial_Tissue_Fertile_Control_15

source_name: Endometrial Tissue, Control, replicate 15


title: Endometrial_Tissue_Fertile_Control_16

source_name: Endometrial Tissue, Control, replicate 16


title: Endometrial_Tissue_Fertile_Control_17

source_name: Endometrial Tissue, Control, replicate 17


title: ITGA2+ trophoblast from K113 donor


title: Endometrial_Tissue_Fertile_Control_14

source_name: Endometrial Tissue, Control, replicate 14


title: HLA-G+ trophoblast from K112 donor


title: EGFR+ trophoblast from K113 donor


title: TDP-43-silenced SK-N-BE cells, biological rep 3 (transcription-level)


title: TDP-43-silenced SK-N-BE cells, biological rep 2 (transcription-level)


title: ITGA2+ trophoblast from K112 donor


title: Sample 8

source_name: S6-T, VEGFA-T dCpf1-BE DNA rep 1


title: Sample 10

source_name: CFTR, S6, VEGFA dCpf1-BE DNA rep 3


title: HLA-G+ trophoblast from K91 donor

value: 9 weeks


title: Sample 9

source_name: RAG1-T, S6-T, VEGFA-T dCpf1-BE DNA rep 2


title: Sample 7

source_name: S3 dCpf1-BE DNA rep 1


title: TDP-43-silenced SK-N-BE cells, biological rep 1 (transcription-level)


title: Sample 6

source_name: RUN dCpf1-BE DNA rep 1 and CDK, DNM, DYR, FAN, S4, EMX, S3 dCpf1-BE DNA rep 2


title: Sample 5

source_name: CDK, DNM, DYR, FAN, RUN, S4, EMX, S3 dCpf1-BE DNA repllicate 3


title: control-silenced SK-N-BE cells, biological rep 3 (transcription-level)

source_name: siCTRL


title: control-silenced SK-N-BE cells, biological rep 2 (transcription-level)


title: Sample 4

source_name: DNM, DYR dCpf1-BE DNA rep 1


title: FUS-silenced SK-N-BE cells, biological rep 1 (transcription-level)

source_name: siFUS


title: Endometrial_Tissue_Fertile_Control_11

source_name: Endometrial Tissue, Control, replicate 11


title: HLA-G+ trophoblast from K85 donor


title: ITGA2+ trophoblast from K91 donor


title: Endometrial_Tissue_Fertile_Control_9

source_name: Endometrial Tissue, Control, replicate 9


title: Endometrial_Tissue_Fertile_Control_12

source_name: Endometrial Tissue, Control, replicate 12


title: Endometrial_Tissue_Fertile_Control_13

source_name: Endometrial Tissue, Control, replicate 13


title: EGFR+ trophoblast from K85 donor

source_name: Placenta


title: EGFR+ trophoblast from K91 donor


title: Sample 2

source_name: S6, VEGFA dCpf1-BE DNA rep 2 and PD1 dCpf1-BE DNA rep 3


title: Sample 3

source_name: CDK, FAN, S4, EMX dCpf1-BE DNA rep 1 and RUN dCpf1-BE DNA rep 2


title: Sample 1

source_name: VEGFA dCpf1-BE DNA rep 1 and CFTR, PD1 dCpf1-BE DNA rep 2


title: Endometrial_Tissue_Fertile_Control_10

source_name: Endometrial Tissue, Control, replicate 10


title: ITGA2+ trophoblast from K85 donor


title: Endometrial_Tissue_Fertile_Control_8

source_name: Endometrial Tissue, Control, replicate 8


title: G1blow ID19

city: Padova

first: Luca

last: Trentin

address: Via Giustiniani, 3

department: Department of Women's and Children's Health

country: Italy

institute: University of Padova

description: Gene expression data from  leukemia samples sorted according to cell cycle annotations

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA

source_name: leukemia cell isolated from spleen of NOD/SCID  mice with full-blown leukemia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng of Total RNA.

growth_protocol: No growth protocol

extract_protocol: RNA was extracted from sorted cells using Trizol.

treatment_protocol: No treatment protocol

tag: cell cycle engrafting time

value: early (G1b early)

tag: cell type


title: Endometrial_Tissue_Fertile_Control_1

source_name: Endometrial Tissue, Control, replicate 1


title: Endometrial_Tissue_Fertile_Control_6

source_name: Endometrial Tissue, Control, replicate 6


title: Endometrial_Tissue_Fertile_Control_5

source_name: Endometrial Tissue, Control, replicate 5


title: G1a ID04

value: late (G2/M)

value: leukemia cell isolated from spleen of NOD/SCID  mice with full-blown leukemia


title: Endometrial_Tissue_Fertile_Control_4

source_name: Endometrial Tissue, Control, replicate 4


title: G1blow ID11


title: G1a ID19


title: Endometrial_Tissue_Fertile_Control_7

source_name: Endometrial Tissue, Control, replicate 7


title: G1a ID012


title: G1a ID11


title: G1blow ID04


title: control-silenced SK-N-BE cells, biological rep 1 (transcription-level)

source_name: siCTRL


title: Endometrial_Tissue_Fertile_Control_3

source_name: Endometrial Tissue, Control, replicate 3


title: Sample 54

source_name: CDK, DNM, DYR, S4, S3 NT DNA rep 2 and EMX NT DNA rep 3

value: DNA

value: NT


title: G1blow ID012


title: Endometrial_Tissue_Fertile_Control_2

source_name: Endometrial Tissue, Control, replicate 2


title: 4sURNA_60_R2

status: Public on Mar 17 2018

city: Lausanne

first: Jennifer

middle: Yihong

last: Tan

address: Rue du Bugnon 27

department: Department of Computational Biology

country: Switzerland

institute: University of Lausanne

library_source: transcriptomic

data_processing:
Hundred nucleotides long single-end stranded reads were mapped to mouse ribosomal RNA sequences with STAR V 2.5.0 (Dobin et al., 2013).
Reads not mapping to ribosomal RNA were then aligned to intronic and exonic sequences using STAR and quantified using RSEM (Li and Dewey, 2011).
Rates of synthesis, processing and degradation were independently inferred using biological duplicates at each labelling points using the INSPEcT Bioconductor package Version 1.8.0 (de Pretis et al., 2015) and biotype differences in the average rate across the 3 labeling times.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data table contains the expression levels of transcript exons and introns (Transcripts Per Million, TPM). Values below expression cutoff (TPM < 1) were converted to NAs and excluded in downstream analysis.

organism: Mus musculus

growth_protocol: Mouse DTCM23/49 XY embryonic stem cell lines (mESCs) were cultured in Knockout Dulbecco’s Modified Eagle Medium (D-MEM, Thermo Fisher, #10829-018) supplemented with 15% fetal bovine serum (FBS, Thermo Fisher, #16000-044), 1% antibiotic penicillin/streptomycin (Thermo Fisher, 15070063), Recombinant mouse LIF protein to a final concentration of 0.01% (Merck, #ESG1107) and 0.06 mM 2-Mercaptoethanol (Thermo Fisher, #31350-010), on 0.1% gelatin-coated cell culture dishes. When confluent, culture was divided in two and passaged 8 times. Five million mESCs of each of these 2 biological replicates were seeded on a 10 cm 0.1% gelatin-coated tissue plate and allowed to grow to 70-80% confluency (approximately 1 day).

extract_protocol:
RNA was extracted using phenol:chloroform:isoamyl alcohol (Sigma, P3803-400ML). Equal volume of biotinylated RNA and prewashed DynabeadsTM MyOneTM Streptavidin T1 beads (Thermo Fischer, 65601) were added to 2X B&W Buffer (10 mM Tris-HCl pH7.5, 1mM EDTA, 2M NaCl (Thermo Fisher, #65601)) and incubated at room temperature for 15 minutes under rotation. The beads were then separated from the mixture using DynaMagTM-2 Magnet (Thermo Fisher, #12321D) and after removal of supernatant, washed with 1X B&W three times. Biotinylated RNA was recovered from the supernatant after 1 minute incubation with RTL buffer (RNeasy kit, Qiagen, #74104) and purified using the RNeasy kit according to manufacturer’s instructions.
Total RNA libraries were prepared from 10 ng of DNAse treated total RNA and newly transcribed RNA using Ovation® RNA-Seq and sequenced on  Illumina HiSeq 2500.

treatment_protocol: 4sU (Sigma, T4509) was added to the growth medium (final concentration of 200 µM) and the cells were incubated at 37 ºC for 15, 30 or 60 minutes. Plates were washed once with 1X PBS and RNA extracted using Trizol (Thermo Fisher, #15596-026). 100 µg of extracted RNA were incubated for 2 h at room temperature with rotation in 1/10 volume of 10X biotinylation buffer (Tris-HCl pH 7.4, 10 mM EDTA) and 2/10 Volume of biotin-HPDP (1mg/ml in Dimethylformamide (Thermo Fisher, #21341)).

tag: rna

value: Labeled

tag: labeling time (min)

tag: biological replicate


title: 4sURNA_15_R2


title: 4sURNA_30_R2


title: LW_22: blood_Large White_22

city: Jouy-en-Josas

first: Marco

last: Moroldo

address: Domaine de Vilvert

department: Animal Genetics

institute: INRA

description: Gene expression Large White

hyb_protocol: Subsequently, for each sample 600 ng of Cy3-labeled cRNA (specific activity > 9.0 pmol Cy3/µg of cRNA) were fragmented at 60°C for 30 minutes in a volume of 25 µl containing 25x of Agilent Fragmentation Buffer and 10x of Agilent Blocking Agent. Afterwards, 25 µl of 2x Agilent Hybridization Buffer were added to the fragmentation mixture and hybridized to the array following the recommended protocol. After hybridization, microarrays were washed 1 minute at room temperature with the GE Wash Buffer 1 (Agilent Technologies) and 1 minute at 37°C using the GE Wash Buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing using a G2565CA Scanner System (Agilent Technologies) using one color scan settings for 8X60K slides

data_processing: The scanned images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09).

organism: Sus scrofa

source_name: blood, Large White, 22

label_protocol: Cyanine-3 (Cy3) labeled cRNAs were prepared using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies), and the starting RNA amounts varied according to the type of sample under analysis. In the case of total RNAs 50 ng were used, while in the case of Co-IP RNAs 10 ng were used. In both cases specific activities and cRNA yields were measured using the NanoDrop ND-1000 (Thermo Fisher Scientific).

extract_protocol: Total RNAs were extracted using the PaxGene Blood RNA Kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendations. RNA yield and purity were measured using a NanoDrop 1000 (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA)

treatment_protocol: Animals were fed an ad libitum standard diet

value: blood

tag: breed

value: Large White

tag: individual


title: LW_09: blood_Large White_09

description: Gene expression Large White

source_name: blood, Large White, 09


title: LW_05: blood_Large White_05

description: Gene expression Large White

source_name: blood, Large White, 05


title: 4sURNA_60_R1


title: 4sURNA_15_R1


title: LW_18: blood_Large White_18

description: Gene expression Large White

source_name: blood, Large White, 18


title: 4sURNA_30_R1


title: LW_07: blood_Large White_07

description: Gene expression Large White

source_name: blood, Large White, 07


title: LW_12: blood_Large White_12

description: Gene expression Large White

source_name: blood, Large White, 12


title: LW_02: blood_Large White_02

description: Gene expression Large White

source_name: blood, Large White, 02


title: LW_15: blood_Large White_15

description: Gene expression Large White

source_name: blood, Large White, 15


title: DD_21: blood_SLAdd_21

description: Gene expression SLAdd

source_name: blood, SLAdd, 21

value: SLAdd


title: totalRNA_60_R2

value: Total


title: LW_24: blood_Large White_24

description: Gene expression Large White

source_name: blood, Large White, 24


title: DD_16: blood_SLAdd_16

description: Gene expression SLAdd

source_name: blood, SLAdd, 16


title: totalRNA_15_R2


title: DD_19: blood_SLAdd_19

description: Gene expression SLAdd

source_name: blood, SLAdd, 19


title: DD_23: blood_SLAdd_23

description: Gene expression SLAdd

source_name: blood, SLAdd, 23


title: LW_14: blood_Large White_14

description: Gene expression Large White

source_name: blood, Large White, 14


title: DD_08: blood_SLAdd_08

description: Gene expression SLAdd

source_name: blood, SLAdd, 08


title: DD_13: blood_SLAdd_13

description: Gene expression SLAdd

source_name: blood, SLAdd, 13


title: LW_04: blood_Large White_04

description: Gene expression Large White

source_name: blood, Large White, 04


title: DD_11: blood_SLAdd_11

description: Gene expression SLAdd

source_name: blood, SLAdd, 11


title: totalRNA_30_R2


title: totalRNA_30_R1


title: DD_10: blood_SLAdd_10

description: Gene expression SLAdd

source_name: blood, SLAdd, 10


title: totalRNA_15_R1


title: DD_06: blood_SLAdd_06

description: Gene expression SLAdd

source_name: blood, SLAdd, 06


title: totalRNA_60_R1


title: Terminal Effector RNA Kaech 1

city: Seattle

first: Robert

middle: Anthony

last: Amezquita

state: WA

address: 1100 Fairview Ave. N.

department: Integrated Immunotherapy Research Center

country: USA

institute: Fred Hutchinson Cancer Research Institute

data_processing:
Preprocessing. All samples were subjected to quality control with FastQC. Subsequently, individual reads had adapters removed and required a phred score of 20 or greater to be retained for for further analysis. Reads were mapped using bowtie2 with –very-sensitive settings. Duplicate reads were removed with Picard. In the case of paired-end data, only concordant mate pairs were retained with a mapping score of greater than 30. For ATAC-seq data, mitochondrial reads were excluded and reads were shifted by +4/-5 basepairs on the positive and negative strands, respectively (Langmead & Salzberg, 2012; Buenrostro et al., 2013).
MACS2 Peak Calling. Peaks were first called for each sample using MACS2 v2.1.0, normalizing relative to input in each case. For punctate marks such as H3K27Ac, H3K4me3, and transcription factors, default macs2 settings were used with inputs if available; for broad marks such as H3K27me3, H3K4me1, the –broad setting was invoked with inputs if available; for ATAC-seq, the –broad setting was invoked along with –nomodel, –shift -100, and –extsize 200. (Y. Zhang et al., 2008)
Read counts were first tallied over the atlas peaksets for each mark per sample using HTSeq, ignoring strand and in union mode (Anders et al., 2015). Subsequently, analysis was performed DESeq2 v1.14.1, with the read counts normalized by fitting the data to a local smoothed dispersion unblinded fit to better capture the observed dispersion-mean relationship and account for batch effects (Love et al., 2014).
Genome_build: GRCm38.p5 (mm10)

source_name: Terminal Effector RNA Kaech

extract_protocol:
ChIP experiments were performed on FACS purified in vivo adoptively transferred P14+ CD8+ T cells. CD8α+CD44+Thy1.1+ cells were sorted based on expression of KLRG1 and IL7Rα to purified populations of TE (KLRG1HiIL7RαLo) and MP (KLRG1LoIL7RαHi) cells. Cells were crosslinked with 1% formaldehyde in 10% fetal bovine serum containing RPMI medium for 10 minutes at 37C. Crosslinking was stopped by addition of 2.5M glycine at 1:20 dilution for 5 minutes at room temperature. Washed cells were lysed and sonicated to obtain chromatin fragments of 150 to 500 base pairs. ChIP was performed on sonicated chromatin from 1-10 million cells with anti- H3K27me3 (Abcam, ab6002), anti-H3K27Ac (Abcam, ab4729), anti-H3K4me3 (Abcam, ab4XXX), and anti-H3K4me1 (Abcam, ab4XXX) antibodies. ATAC-seq library preparations were performed as described in (Buenrostro et al., 2013). Immunoprecipitated DNA was purified, amplified, processed into a library, and sequenced on an Illumina HiSeq 2500 with 4 samples per lane (170M reads are distributed at 42.5M reads per sample with 75bp reads in single-end mode).
Total RNA was purified with the use of a Qiazol and RNeasy Mini kit (Qiagen), in which on-column treatment with DNase was included. Purified RNA was submitted to the Yale Center for Genomic Analysis, where it was subjected to isolation of mRNA and library preparation. Libraries were pooled, six samples per lane, and were sequenced on an Illumina HISEQ 2500 (75–base pair paired- end reads), followed by alignment and quantification with Kallisto using the GRCm38 (mm10) reference genome. Counts were imported and normalized with DESeq2 v1.14.1, with the read counts normalized by fitting the data to a local smoothed dispersion in an unblinded fit to better capture the observed dispersion-mean relationship and account for batch effects, and subsequently used to perform differential expression analysis (Love et al., 2014).

value: CD8+ T cells

tag: cell subset

value: Terminal Effector

tag: assay

value: RNA

tag: lab

value: Kaech

tag: run

tag: librarylayout

value: PAIRED

tag: replicate


title: Special Tbet Kaech 1

description:
Please note that a duplicated run record (of the existing SRR2075567) was created and linked to the current sample for the convenient retrieval of the complete raw data from SRA
S_Tbet_Kaech_1

source_name: Special Tbet Kaech

value: Special

value: Tbet

value: SINGLE

tag: chip antibody

value: anti-T-bet

tag: chip antibody vendor/cat. #

value: Santa Cruz


title: Terminal Effector H3K4me3 Kaech 1

source_name: Terminal Effector H3K4me3 Kaech

value: Abcam, ab8580


title: Terminal Effector Input Kaech 1

source_name: Terminal Effector Input Kaech

value: Input

value: none (Input)


title: Terminal Effector H3K4me3 Kaech 2


title: Terminal Effector RNA Kaech 2


title: Special Tbet Kaech 2

description:
Please note that a duplicated run record (of the existing SRR2075568) was created and linked to the current sample for the convenient retrieval of the complete raw data from SRA
S_Tbet_Kaech_2


title: Terminal Effector Input Kaech 2


title: Terminal Effector ATAC Kaech 2

source_name: Terminal Effector ATAC Kaech

value: ATAC


title: Terminal Effector H3K27ac Kaech 1

source_name: Terminal Effector H3K27ac Kaech

value: Abcam, ab4729


title: Memory Precursor RNA Kaech 3

source_name: Memory Precursor RNA Kaech

value: Memory Precursor


title: Memory Precursor RNA Kaech 2


title: Terminal Effector RNA Kaech 3


title: Terminal Effector H3K27me3 Kaech 1

source_name: Terminal Effector H3K27me3 Kaech

value: Abcam, ab6002


title: Terminal Effector H3K27me3 Kaech 2

value: CD8+ T cells


title: Terminal Effector H3K27ac Kaech 2

value: Terminal Effector


title: Terminal Effector ATAC Kaech 3


title: DD_01: blood_SLAdd_01

description: Gene expression SLAdd

source_name: blood, SLAdd, 01

tag: tissue

value: blood

value: SLAdd


title: Memory Precursor Input Kaech 2

source_name: Memory Precursor Input Kaech

value: Kaech


title: Memory Precursor RNA Kaech 1

value: RNA

value: PAIRED


title: Terminal Effector ATAC Kaech 1

value: SINGLE


title: Memory Precursor H3K4me3 Kaech 1

source_name: Memory Precursor H3K4me3 Kaech


title: Memory Precursor Input Kaech 1


title: Memory Precursor H3K4me3 Kaech 2


title: Memory Precursor H3K27me3 Kaech 1

source_name: Memory Precursor H3K27me3 Kaech


title: Memory Precursor H3K27ac Kaech 2

source_name: Memory Precursor H3K27ac Kaech


title: Effector Input Kaech 3

source_name: Effector Input Kaech

value: Effector


title: Memory Precursor ATAC Kaech 3

source_name: Memory Precursor ATAC Kaech


title: Effector RNA Kaech 1

source_name: Effector RNA Kaech


title: Memory Precursor H3K27ac Kaech 1


title: Effector Input Kaech 1


title: Effector Input Kaech 2


title: Effector RNA Kaech 3


title: Effector H3K27me3 Kaech 2

source_name: Effector H3K27me3 Kaech


title: Memory Precursor H3K27me3 Kaech 2


title: Effector RNA Kaech 2


title: Effector H3K4me1 Kaech 2

source_name: Effector H3K4me1 Kaech

value: Abcam, ab8895


title: Effector H3K27me3 Kaech 1


title: Effector H3K27me3 Kaech 3


title: Memory Precursor ATAC Kaech 2


title: Effector Input Kaech 5


title: Effector Input Kaech 4


title: Effector H3K4me3 Kaech 2

source_name: Effector H3K4me3 Kaech

value: Abcam, ab8580


title: Memory Precursor ATAC Kaech 1


title: Effector H3K27me3 Kaech 4


title: Effector H3K4me1 Kaech 1


title: Effector H3K27ac Kaech 3

source_name: Effector H3K27ac Kaech


title: Effector H3K27ac Kaech 2


title: Effector H3K27ac Kaech 5


title: Naive RNA Kaech 3

source_name: Naive RNA Kaech

value: Naive


title: Naive RNA Kaech 2


title: Effector H3K27ac Kaech 4


title: Naive Input Kaech 1

source_name: Naive Input Kaech

value: Input

value: none (Input)


title: Naive Input Kaech 2


title: Naive RNA Kaech 1


title: Naive H3K4me3 Kaech 2

source_name: Naive H3K4me3 Kaech


title: Naive H3K4me1 Kaech 2

source_name: Naive H3K4me1 Kaech


title: Naive H3K4me3 Kaech 1


title: Naive H3K27me3 Kaech 2

source_name: Naive H3K27me3 Kaech


title: Naive H3K4me1 Kaech 1


title: Naive H3K27ac Kaech 2

source_name: Naive H3K27ac Kaech

value: Abcam, ab4729


title: Naive H3K27ac Kaech 1


title: Naive ATAC Kaech 3

source_name: Naive ATAC Kaech

value: ATAC


title: Naive ATAC Kaech 2


title: Naive ATAC Kaech 1


title: Effector H3K27ac Kaech 1


title: Naive H3K27me3 Kaech 1

value: Abcam, ab6002


title: Epiblast of E7.5

city: Jinan

first: Xukun

last: Lu

address: No. 44 Wenhua West Road

institute: Shandong University

description: Gene expression data of E7.5 mouse epiblast

hyb_protocol: Fragmented cRNAs were hybridized for 16 hours at 45℃. Then Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The raw hybridization data were analyzed using Affymetrix GeneChip Command Console Software (AGCC). The Robust Multiarray Average (RMA) method was used for background correction and data normalization, and the affy suite of the bioconductor package (http://www.bioconductor.org) was used to calculate expression values. Significance Analysis of Microarrays (SAM) was used to identify genes that are differentially expressed.

source_name: E7.5 epiblast

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

extract_protocol: Total RNA from each germ layer sample was prepared using RNeasy Micro Kit (Qiagen, 74004) according to the manufacturer’s instruction and treated with DNase I to remove residual genomic DNA.

value: Epiblast

tag: developmental stage

tag: strain

value: ICR


title: Mesoderm of E7.5

description: Gene expression data of E7.5 mouse mesoderm

source_name: E7.5 mesoderm

value: Mesoderm


title: Endoderm of E7.5

description: Gene expression data of E7.5 mouse endoderm

source_name: E7.5 endoderm

value: Endoderm


title: Misthi_doxorubucin_rep1

city: Tokyo

first: Yoku

last: Hayakawa

state: TOKYO

address: 7-3-1, Hongo, Bunkyo-ku, Clinical Research Center 4F, Room 425

country: Japan

institute: University of Tokyo

description: Doxorubicn-treated Mist1+CD24hi cells

hyb_protocol: Following fragmentation, 6.6 ug of biotinylated cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS5) using Affymetrix Expresson Console Software (ThermoFisher Scientific) according to the default analysis settings.

source_name: Mist1+CD24hi, doxorubucin

label_protocol: Biotinylated 2nd-Cycle ds-cDNA were prepared using GeneChip Pico Kit (ThermoFisher Scientific) according to the standard manufacturer's protocol from 0.8 ng total RNA.

extract_protocol: Ambion RNA extraction kit

value: small intestine

tag: cell type


title: Mistlo_doxorubucin_rep1

description: Doxorubicn-treated Mist1+CD24lo cells

source_name: Mist1+CD24lo, doxorubucin


title: Mistlo_doxorubucin_rep2

description: Doxorubicn-treated Mist1+CD24lo cells


title: Misthi_NICD_rep1

description: NICD+Mist1+CD24hi cells

source_name: Mist1+CD24hi, NICD


title: Misthi_doxorubucin_rep2

description: Doxorubicn-treated Mist1+CD24hi cells


title: Misthi_untreated_rep2

description: Untreated Mist1+CD24hi cells

source_name: Mist1+CD24hi, control


title: Mistlo_irradiation_rep1

description: Irradiated Mist1+CD24lo cells

source_name: Mist1+CD24lo, 10Gy


title: Misthi_irradiation_rep1

description: Irradiated Mist1+CD24hi cells

source_name: Mist1+CD24hi, 10Gy


title: Mistlo_DT_rep2

description: Lgr5-ablated Mist1+CD24lo cells

source_name: Mist1+CD24lo, Lgr5-ablated


title: Whole intestine

description: Whole intestine sample

source_name: Whole intestine

value: villi


title: Misthi_NICD_rep2

description: NICD+Mist1+CD24hi cells


title: Mistlo_DT_rep1

description: Lgr5-ablated Mist1+CD24lo cells


title: Misthi_untreated_rep1

description: Untreated Mist1+CD24hi cells


title: Misthi_irradiation_rep2

description: Irradiated Mist1+CD24hi cells


title: Misthi_DT_rep2

description: Lgr5-ablated Mist1+CD24hi cells

source_name: Mist1+CD24hi, Lgr5-ablated


title: Mistlo_NICD_rep1

description: NICD+Mist1+CD24lo cells

source_name: Mist1+CD24lo, NICD


title: Mistlo_irradiation_rep2

description: Irradiated Mist1+CD24lo cells


title: Misthi_DT_rep1

description: Lgr5-ablated Mist1+CD24hi cells


title: Mistlo_NICD_rep2

description: NICD+Mist1+CD24lo cells


title: Mistlo_untreated_rep1

description: Untreated Mist1+CD24lo cells

source_name: Mist1+CD24lo, control


title: Mistlo_untreated_rep2

description: Untreated Mist1+CD24lo cells


title: G42_Tat+Meth-

city: San Diego

first: Maria

middle: Cecilia

last: Marcondes

state: CA

address: 3525 John Hopkins Ct. #200

institute: San Diego Biomedical Research Institute

description: m1958 - G4 Tat+Meth-

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing:
The analysis was performed by Phalanx analysis service.
They used Rosetta Resolver system (Rosetta software) to process the analysis, using profile error model calculation.
The normalized intensities were obtained with median scaling, performed on data set without flagged and control data.
PCA and clustering analysis were by averagely linkage algorithm performed on selected expressed gene lists after log 2 transformation and mean centering, in Matlab.

source_name: Tat+Meth-

label_protocol: Agilent Low input quick Amp labelling kit

extract_protocol: RNA was extracted using RNAeasy (Qiagen) kit, quantifyed in Nanodrop

treatment_protocol: Left hemisphere of perfused brain

tag: strain background

tag: Sex

value: male

tag: age

value: 6-7 weeks

tag: genotype/variation

value: containing both the GFAP promotor-controlled Tet-binding protein and the TRE promoter-TAT protein transgene (TAT+)

tag: tat expression

tag: treated with

value: saline (0.9%)

value: brain


title: G41_Tat+Meth-

description: m1942 - G4 Tat+Meth-


title: G44_Tat+Meth-

description: m1971 - G4 Tat+Meth-


title: G45_Tat+Meth-

description: m1972 - G4 Tat+Meth-


title: G43_Tat+Meth-

description: m1959 - G4 Tat+Meth-


title: G15_Tat-Meth+

description: m2069 - G1 Tat-Meth+

source_name: Tat-Meth+

value: containing the GFAP promoter-controlled Tet-binding protein (TAT−)

value: 2 mg/kg methamphetamine


title: G31_Tat+Meth+

description: m1962 - G3 Tat+Meth+

source_name: Tat+Meth+


title: G35_Tat+Meth+

description: m2201 - G3 Tat+Meth+


title: G33_Tat+Meth+

description: m1975 - G3 Tat+Meth+


title: G25_Tat-Meth-

description: m2021 - G2 Tat-Meth-

source_name: Tat-Meth-


title: G34_Tat+Meth+

description: m2005 - G3 Tat+Meth+


title: Effector H3K4me3 Kaech 1

source_name: Effector H3K4me3 Kaech

value: CD8+ T cells

tag: cell subset

value: Effector

tag: assay

value: Kaech

value: SINGLE

value: Abcam, ab8580


title: PSM6XC14

city: Boston

first: Curtis

last: Huttenhower

state: MA

address: 677 Huntington Ave

department: Biostatistics

institute: Harvard T.H. Chan School of Public Health

data_processing:
Transcripts were aligned to hg19 using topHat v2.0.14 and then resolved to counts using htseq-count version 0.6.1. Sample quality was assessed on the basis of percentages of tags mapping to exonic vs non exonic regions. If the percent of reads mapping to a non-exonic region was > 40% it was considered a QC fail. No samples failed by this metric.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited gene count tables as generated by htseq-count

source_name: rectum tissue

extract_protocol:
Medium with the biopsy samples poured into a 100 mm Petri dish from which tissue was transferred to a new clean 40 mm Petri dish using forceps. Biopsy tissue is minced with fine dissection scissors and pipetted using a P1000 pipette into a 5 mL Eppendorf tube. An additioanl 4 mL washing medium plus 10 µM ROCK inhibitor (Y-27632) was then added to Eppendorf tube.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: biopsy location

value: Rectum

tag: disease status

value: Non IBD

tag: gender

value: Female


title: PSM7J4EX

source_name: intestinal tissue

value: Ileum

value: Ulcerative Colitis

value: Male


title: PSM7J4EW


title: G21_Tat-Meth-

description: m1944 - G2 Tat-Meth-

value: male

value: 6-7 weeks


title: PSM6XC13


title: PSM6XC11


title: PSM7J4F4

value: Crohn's Disease


title: PSM7J4FL


title: PSM7J4EU


title: PSM7J4F3


title: PSM7J4EV


title: G12_Tat-Meth+

description: m1951 - G1 Tat-Meth+

value: brain


title: G23_Tat-Meth-

description: m1957 - G2 Tat-Meth-

value: containing the GFAP promoter-controlled Tet-binding protein (TAT−)

value: saline (0.9%)


title: G13_Tat-Meth+

description: m2002 - G1 Tat-Meth+

value: 2 mg/kg methamphetamine


title: G24_Tat-Meth-

description: m2020 - G2 Tat-Meth-


title: G14_Tat-Meth+

description: m2007 - G1 Tat-Meth+


title: G32_Tat+Meth+

description: m1963 - G3 Tat+Meth+

value: containing both the GFAP promotor-controlled Tet-binding protein and the TRE promoter-TAT protein transgene (TAT+)


title: G11_Tat-Meth+

description: m1950 - G1 Tat-Meth+


title: PSM6XBZZ


title: PSM6XBZW


title: PSM6XBZY


title: PSM6XC15

source_name: colon tissue

value: Transverse colon


title: PSM6XBZQ


title: PSM6XBZO


title: PSM6XBZR


title: PSM6XBZP


title: PSM6XBZI


title: PSM6XBZX


title: MSM719NO


title: MSM719MU


title: MSM719NA


title: MSM719MR


title: MSM719NP


title: MSM719N1


title: PSM6XBZJ


title: MSM719MS


title: MSMAKNES


title: MSMAKNET

value: Ascending (right-sided) colon


title: MSM719MD


title: MSM719ME


title: MSM719MT


title: MSM719MA


title: MSM5LWKF


title: MSM5LWKG


title: MSM5LWJU


title: MSM5LWJS


title: MSM5LWJV


title: MSM5LWJT


title: MSM719M5


title: MSM5LWJO


title: PSM6XBZD


title: PSM6XBZC


title: MSM5LWJH


title: MSM719MZ


title: MSM5LWJN


title: MSM5LWJG


title: MSM719N5


title: MSM5LWJ3


title: MSM5LWL6


title: MSM719N4


title: MSM5LWL1


title: MSM5LWL4


title: MSM719M6


title: MSM5LWKR

value: Cecum


title: MSM5LWL5


title: MSM5LWJ4

value: Rectum


title: MSM5LWL3


title: MSM5LWL7


title: MSM5LWKX


title: MSM5LWKQ


title: MSM5CFD7


title: MSM5CFD6


title: MSM5LWJZ


title: MSM5LWKE

value: Descending (left-sided) colon


title: MSM5LWKW


title: MSM5LWKD

value: Female


title: MSM5CFCW


title: MSM5CFCU


title: MSM5LWL2


title: MSM5CFCV

value: Ileum


title: HSM9UBMT

value: Non IBD


title: HSM9UBMU


title: HSM9UBMS


title: HSM9UBMP


title: HSM9UBMQ

value: Ulcerative Colitis

value: Male


title: HSM9UBMR


title: HSM9UBMN


title: HSM9JTC7


title: HSM9JTC8


title: HSM9UBMO


title: HSM9JTC2

source_name: tissue

value: Non-inflamed


title: HSM9JTC3


title: HSM9JBU

value: Crohn's Disease


title: HSM9JBV


title: HSM9JTBZ


title: HSM9JTC1


title: HSM9JBW


title: HSM9JTBX


title: HSM7H3WW


title: HSM7H3WY


title: HSM7H3WP


title: HSM7H3WX


title: HSM7H3WN


title: HSM7H3WL


title: HSM7H3WO

value: Sigmoid Colon


title: HSM7H3WM


title: HSM7H3WK


title: HSM6S4GJ


title: HSM7H3WH


title: HSM6S4GL


title: HSM6S4GK


title: HSM7H3WJ


title: HSM6S4GI


title: HSM6S4G5


title: HSM6S4GH


title: HSM9JTBY


title: HSM6S4GG


title: HSM6S4G6


title: HSM6S4G4


title: HSM6S4G7


title: HSM6S4G3


title: HSM6S4FZ


title: HSM6S4G2


title: HSM6S4FT


title: HSM6S4G1


title: HSM6S4FU


title: HSM6S4FY


title: HSM6S4GQ


title: HSM6S4GP


title: HSM6S4GO


title: HSM6S4FQ


title: HSM6S4FO


title: HSM6S4FS


title: HSM6S4FR


title: HSM6S4FN


title: HSM5FZAS


title: G22_Tat-Meth-

description: m1952 - G2 Tat-Meth-

value: male

value: 6-7 weeks

value: containing the GFAP promoter-controlled Tet-binding protein (TAT−)

value: brain


title: HSM6S4FP


title: HSM5FZAT


title: HSM5FZAW

value: Transverse colon


title: HSM5FZAU

value: Ascending (right-sided) colon


title: HSM5FZAV


title: HSM5FZAX


title: HSM5FZAY


title: HSM5FZAZ


title: HSM5FZB2


title: HSM5FZB1


title: HSM5FZB4


title: PSM6XC12


title: HSM5FZBB


title: HSM5FZB5


title: HSM5FZBC


title: HSM5FZBD


title: HSM5FZBE


title: HSM6S4GM


title: HSM6S4GN


title: HSM5FZBH


title: HSM5FZBI


title: HSM6S4GC


title: HSM5FZBF


title: HSM5FZBG


title: HSM6S4GB


title: HSM5FZAR


title: HSM5FZAQ


title: HSM7H3WQ


title: HSM7H3WR


title: HSM5FZAN


title: HSM5FZAM


title: HSM5FZAE


title: ESM5GEY7


title: HSM7H3WS


title: HSM5FZAH


title: HSM5FZB3


title: ESM5GEYA


title: ESM5GEY8


title: ESM6ZK8Z

value: Cecum


title: ESM5GEY9


title: ESM5GEYK


title: ESM5GEYL

value: Rectum


title: ESM5GEYI


title: CSMDRVXZ


title: CSMDRVY4

value: Terminal ileum


title: CSMDRVY5

value: Female


title: CSMDRVY6


title: CSMDTZ4X


title: CSMDRVY1


title: CSMDRVY7


title: CSMDRVXX

value: Ileum


title: ESM5GEYB


title: CSMDRVY2


title: CSMDRVXU


title: CSMDRVXY


title: CSMDRVXR


title: CSMDRVXS


title: CSMDRVXP


title: CSMDRVXO


title: Cbf1 replicate 3 TF-bound fraction

city: Stanford

first: Polly

middle: Morrell

last: Fordyce

address: 443 Via Ortega

department: Genetics, Bioengineering

institute: Stanford University

data_processing:
Library strategy: BET-Seq
All data processed using custom scripts available from https://github.com/FordyceLab/BET-seq
1. There is no extraction protocol, the library is made of fully synthetic DNA. Synthesis protocol and library construction protocol are included in the file below (excepted from our manuscript's Supporting Information section).
2. Generally, the data processing steps following sequencing are filtering only reads with average PHRED score > 30, extraction of flanking sequences and unique molecular identifiers through the use of regular expressions, and deduplication by extraction of only unique UMI/flanking sequence pairs in each library (generalized custom Python script included in the GitHub repository which we have now made public - https://github.com/ FordyceLab/BET-seq/blob/master/data_processing.py). The resultant processed data file (counts.txt) contains the following columns:
*  flank - concatenated sequence flanking the "CACGTG" e-box motif
*  tf_count - deduplicated read count in the transcription factor-enriched sublibrary
*  ref_count - deduplicated read count in the input sublibrary
*  tf - total read-normalized probability for each flank in the transcription factor-enriched sublibrary
*  ref - total read-normalized probability for each flank in the input sublibrary
*  ddG - scaled delta delta G value for each flanking sequence (-log(tf/ref)\*R*T*scalar) where the scalar is determined by orthogonal measurement (see manuscript for further explanation - https://www.biorxiv.org/content/early/2017/09/26/193904)
*  protein - transcription factor used for enrichment step
*  rep - experimental replicate number

organism: synthetic construct

source_name: synthetic DNA

extract_protocol: Synthesis, amplicon sequencing

tag: experiment

value: Cbf1  TF-bound fraction


title: CSMDRVXL

value: Ulcerative Colitis


title: CSMDRVXM

value: Male


title: Pho4 replicate 4 TF-bound fraction

value: Pho4  TF-bound fraction


title: CSMDRVXK


title: CSMDRVY3

value: Crohn's Disease


title: CSMDRVXN

value: Descending (left-sided) colon


title: CSMDRVXJ


title: CSMDRVXH

value: Sigmoid Colon


title: CSMDRVXG


title: CSMDRVXI


title: CSM5FZ3B


title: CSMDRVXQ


title: CSMDTZ4Y


title: CSM5FZ38

value: Non IBD


title: CSMDRVXT


title: Input fraction for Pho4 replicates 3, 4 and Cbf1 replicates 2,3

value: Input fraction for Pho4  and Cbf1


title: CSM5FZ34


title: CSM5FZ39


title: CSM5FZ36


title: CSM5FZ3C


title: MSM719MJ


title: Pho4 replicate 3 TF-bound fraction


title: CSM5FZ2S


title: CSM5FZ2R


title: CSM5FZ2T


title: CSM5FZ3A


title: CSMDRVXF


title: CSM5FZ37


title: CSM5FZ2Q


title: CSM5FZ35


title: CSM5FZ2P


title: rat fed low corn oil diet, biological rep1

city: Cartagena

first: Niradiz

last: Reyes

address: Campus de Zaragocilla. Facultad de Medicina

country: Colombia

institute: Universidad de Cartagena

description: Gene expression data from prostate of ACI rats fed low corn oil diet for 18 months

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome U34 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Rattus norvegicus

source_name: ACI rat fed a low corn oil diet for 18 months, biological replicate 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: male ACI rats were placed on either a high corn oil diet or a low corn oil diet for 18 months.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: dorsolateral prostates were resected at the end of the 18 month treatment and half was used for RNA extraction and hybridization to affymetrix microarrays and the other half was used for histochemical and immunohistochemical analysis

value: dorsolateral prostate

value: ACI

value: 18 month old

value: male


title: rat fed high corn oil diet, biological rep3

source_name: ACI rat fed a high corn oil diet for 18 months, biological replicate 3


title: rat fed low corn oil diet, biological rep2

source_name: ACI rat fed a low corn oil diet for 18 months, biological replicate 2


title: rat fed low corn oil diet, biological rep3

source_name: ACI rat fed a low corn oil diet for 18 months, biological replicate 3


title: rat fed high corn oil diet, biological rep1

description: Gene expression data from prostate of ACI rats fed high corn oil diet for 18 months

source_name: ACI rat fed a high corn oil diet for 18 months, biological replicate 1


title: CSM5FZ2O


title: rat fed high corn oil diet, biological rep2

source_name: ACI rat fed a high corn oil diet for 18 months, biological replicate 2


title: CSM5FZ2M

value: Rectum


title: CSM5FZ2L


title: CSM5FZ2N

value: Cecum


title: Stretched_NRVMs_24h_rep_04

city: Kuopio

first: Jaana

last: Rysae

address: Yliopistonranta 1C

department: School of Pharmacy

country: Finland

institute: University of Eastern Finland

description: Gene expression data from stretched neonatal rat ventricular myocytes

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Robust Multichip Average (RMA) normalization was performed, and quantile normalization, and baseline transformed to median of all samples in GeneSpring 12.6 Software

source_name: Neonatal rat ventricular myocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: Neonatal rat ventricular myocytes were prepared from 2-4 days old Sprague-Dawley rats as previously described (Pikkarainen et al.J. Biol. Chem. 278, 23807–23816 (2003).

extract_protocol: Total RNA was isolated using Tisolated with TRIzol Reagent (Sigma Aldrich) according to the manufacturer’s protocol (Invitrogen) by using the Phase Lock Gel system (Eppendorf).

treatment_protocol: Stretch was introduced to cells by applying a cyclic vacuum suction under the flexible bottomed plates by computer-controlled equipment (Flexercell Strain Unit FX-3000, Flexcell).

value: Sprague-Dawley

tag: treatment

value: 24h stretch


title: Stretched_NRVMs_48h_rep_04

value: 48h stretch


title: Stretched_NRVMs_48h_rep_03


title: CSM5FZ2H

value: Ulcerative Colitis

value: Female


title: Stretched_NRVMs_48h_rep_02


title: Stretched_NRVMs_48h_rep_05


title: Stretched_NRVMs_24h_rep_03


title: Stretched_NRVMs_24h_rep_05


title: CSM5FZ2G

value: Ileum


title: Stretched_NRVMs_24h_rep_02


title: Stretched_NRVMs_control_rep_04b

description: Gene expression data from control, non-stretched neonatal rat ventricular myocytes

value: control


title: Stretched_NRVMs_control_rep_05b


title: CSM5FZ2F

value: Crohn's Disease


title: CSM5FZ2E


title: Stretched_NRVMs_48h_rep_01


title: Stretched_NRVMs_control_rep_01b


title: Stretched_NRVMs_12h_rep_04

value: 12h stretch


title: Stretched_NRVMs_24h_rep_01


title: Stretched_NRVMs_12h_rep_05


title: Stretched_NRVMs_control_rep_02b


title: CSM5FZ2I

value: Sigmoid Colon


title: Stretched_NRVMs_12h_rep_01


title: Stretched_NRVMs_control_rep_03b


title: Stretched_NRVMs_12h_rep_03


title: Stretched_NRVMs_12h_rep_02


title: Stretched_NRVMs_4h_rep_05

value: 4h stretch


title: Stretched_NRVMs_4h_rep_03


title: Stretched_NRVMs_4h_rep_04


title: CSM5FZ2D


title: Stretched_NRVMs_4h_rep_02


title: CSM5FZ2B


title: Stretched_NRVMs_4h_rep_01


title: CSM5FZ2C


title: CSM5FZ2A


title: HT29_48h_MIRTX

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: HT29 cells overexpressed MIRTX for 48 hours

hyb_protocol: Before hybridization, 1,650 ng labeled cRNA was fragmented and mixed with hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65˚C. The slides were washed according to the manufacturer's manual.

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

source_name: 48h_MIRTX transfected HT29 cells

label_protocol: 200 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

growth_protocol: DLD1 and HT29 cell lines were obtained from the American Type Culture Collection (Rockville, MD) and cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (Sigma, St. Louis, MO) at 37 °C in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol: Total RNA from the transfected DLD1 and HT29 cells were extracted using miRNeasy kit (Qiagen) following manufacturer's instructions. The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA)..

treatment_protocol: DLD1 and HT29 cells were transfected with miR-29b-3p, MIRTX and negative control miRNA. The cells were incubated for 24 and 48 h and collected for RNA extraction, respectively.

tag: cell line

value: HT29 (colorectal adenocarcinoma cell lines)


title: Mes_RNA-seq

data_processing:
Adapters, unknown or low quality bases are removed from the raw reads to generate the clean reads
Clean reads were mapped to reference genome and genes sequences respectively using SOAP2 (Li, 2009)
The abundance of a gene is calculated using RPKM method (Reads Per kb per Million reads) (Mortazavi, Williams et al. 2008)
Differentially expressed genes were analyzed as previously reported with a P-value, and a false discovery rate (FDR) to correct for the P-value (Audic and Claverie, 1997; Benjamini and Hochberg, 1995; Benjamini and Yekutieli, 2001).
For alternative splicing analysis, alternative splicing (AS) patterns were analyzed using ASD software as previously described (Wu et al., 2017; Zhou et al., 2014). Briefly, the clean reads were mapped to the mouse genome (mm10) by TopHat. The generated bam files that were sorted and indexed were imported and analyzed using the ASD software. Eight modes of AS events for the three germ layers were obtained with an adjusted P-value and false discovery rate (FDR).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include gene-level Uniq_reads_num, Length, coverage % and RPKM values. Alternative splicing data analysis is available on the series record.

source_name: Mesoderm of E7.5 mouse embryo

extract_protocol:
Total RNA from each germ layer sample was prepared using RNeasy Micro Kit (Qiagen, 74004) according to the manufacturer’s instruction and treated with DNase I to remove residual genomic DNA.
Libraries for paired-end sequencing were prepared using BGI Kit (Beijing Genomics Institute, Beijing, China)

tag: tissue

value: Mesoderm

tag: developmental stage

value: ICR


title: Stretched_NRVMs_1h_rep_05

tag: strain

value: 1h stretch


title: CSM5FZ29


title: End_RNA-seq

source_name: Endoderm of E7.5 mouse embryo

value: Endoderm


title: CSM5FZ27


title: CSM5FZ28

value: Rectum


title: CSM5FZ23


title: Stretched_NRVMs_1h_rep_03

value: Sprague-Dawley


title: Stretched_NRVMs_1h_rep_01


title: Stretched_NRVMs_1h_rep_02


title: HT29_48h_miR-29b-3p

description: HT29 cells overexpressed miR-29b-3p for 48 hours

source_name: 48h_miR-29b-3p transfected HT29 cells


title: Stretched_NRVMs_control_rep_05a


title: DLD1_48h_miR-29b-3p

description: DLD1 cells overexpressed miR-29b-3p for 48 hours

source_name: 48h_miR-29b-3p transfected DLD1 cells

value: DLD1 (colorectal adenocarcinoma cell lines)


title: DLD1_48h_MIRTX

description: DLD1 cells overexpressed MIRTX for 48 hours

source_name: 48h_MIRTX transfected DLD1 cells

treatment_protocol: DLD1 and HT29 cells were transfected with miR-29b-1-5p, miR-29b-3p, MIRTX and negative control miRNA. The cells were incubated for 24 and 48 h and collected for RNA extraction, respectively.


title: Stretched_NRVMs_control_rep_04a


title: Stretched_NRVMs_control_rep_02a


title: Epi_RNA-seq

source_name: Epiblast of E7.5 mouse embryo

value: Epiblast


title: Stretched_NRVMs_control_rep_03a


title: Stretched_NRVMs_control_rep_01a


title: Stretched_NRVMs_48h_rep_03

description: MicroRNA expression data from stretched neonatal rat ventricular myocytes

hyb_protocol: Hybridization was performed by Exiqon according to manufacturer protocol.

scan_protocol: Scanning was performed by Exiqon according to manufacturer protocol.

data_processing: Data processing was performed by Exiqon according to manufacturer protocol; in brief normalization included background subtraction and normalization with global Lowess (Locally Weighter Scatterplot Smoothing) regression algorithm. This within-slide normalization was performed to minimize differences between the colors in an intensity-dependent manner. The criterion for deciding that a miRNA had failed on a particular array was the observation that 2 or more of the 4 replicated measures of this miRNA had a signal that was below background. In addition, Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide were excluded. Replicated measurements of the same miRNA from each slide were averaged to per-chip median values and then used to obtain geometric means and standard deviations for each miRNA.

label_protocol: Labeling was performed by Exiqon, according to manufacturer protocol; in brief 2 ug of total RNA was labeled using the miRCURY Hy3/Hy5 labeling kit according to Exiqon protocol (Vedbaek, Denmark).

value: 2-4 days old

tag: cell type

value: ventricular myocytes

value: 48h stretch

source_name: common reference pool

tag: source

value: common reference pool


title: Stretched_NRVMs_48h_rep_02

tag: age


title: DLD1_24h_miR-29b-3p

description: DLD1 cells overexpressed miR-29b-3p for 24 hours

source_name: 24h_miR-29b-3p transfected DLD1 cells


title: DLD1_24h_MIRTX

description: DLD1 cells overexpressed MIRTX for 24 hours

source_name: 24h_MIRTX transfected DLD1 cells


title: DLD1_24h_NC_miRNA

description: DLD1 cells overexpressed negative control miRNA for 24 hours

source_name: 24h_Negative control miRNA transfected DLD1 cells


title: Stretched_NRVMs_48h_rep_01


title: DLD1_48h_NC_miRNA

description: DLD1 cells overexpressed negative control miRNA for 48 hours

source_name: 48h_Negative control miRNA transfected DLD1 cells


title: CSM5FZ22

source_name: intestinal tissue

value: Ileum

value: Crohn's Disease

value: Female


title: Stretched_NRVMs_1h_rep_04


title: CSM5FZ1T

value: Ulcerative Colitis

value: Male


title: CSM5FZ1W

source_name: colon tissue

value: Sigmoid Colon


title: CSM5FZ24

source_name: rectum tissue


title: CSM5FZ1S


title: Stretched_NRVMs_24h_rep_01

value: 24h stretch


title: Stretched_NRVMs_control_rep_03 b

description: MicroRNA expression data from control, non-stretched neonatal rat ventricular myocytes

value: control


title: Stretched_NRVMs_24h_rep_03


title: Stretched_NRVMs_24h_rep_02


title: CSM5FZ1Q


title: CSM5FZ1R


title: Stretched_NRVMs_control_rep_02 b


title: Stretched_NRVMs_control_rep_01 b


title: Stretched_NRVMs_12h_rep_03

value: 12h stretch


title: Cbf1 replicate 2 TF-bound fraction

source_name: synthetic DNA

value: Cbf1  TF-bound fraction


title: CSM5FZ1N

value: Rectum


title: Stretched_NRVMs_12h_rep_02

source_name: Neonatal rat ventricular myocytes

value: Sprague-Dawley


title: CSM5FZ1M


title: Cbf1 replicate 1 input fraction

value: Cbf1  input fraction


title: CSM5FZ1V


title: CSM5FZ1U


title: Cbf1 replicate 1 TF-bound fraction


title: CSM5FZ1O


title: Stretched_NRVMs_4h_rep_03

value: 2-4 days old

value: 4h stretch


title: CSM5FZ1L


title: Pho4 replicate 2 TF-bound fraction

value: Pho4  TF-bound fraction


title: Stretched_NRVMs_12h_rep_01

value: ventricular myocytes

value: common reference pool


title: CSM5FZ1K


title: Pho4 replicate 2 input fraction

value: Pho4  input fraction


title: Stretched_NRVMs_4h_rep_02


title: Stretched_NRVMs_4h_rep_01


title: CSM5FZ1J

value: Ileum

value: Female


title: Stretched_NRVMs_1h_rep_02

value: 1h stretch


title: CSM5FZ1H

value: Sigmoid Colon

value: Crohn's Disease


title: Pho4 replicate 1 TF-bound fraction


title: Stretched_NRVMs_1h_rep_01


title: CSM5FZ1I


title: Pho4 replicate 1 input fraction


title: CSM5FZ1F


title: Pho4 replicate 1 GFP control

value: Pho4  GFP control


title: Stretched_NRVMs_control_rep_02

value: control


title: Cbf1 replicate 1 GFP control

value: Cbf1  GFP control


title: Stretched_NRVMs_control_rep_03


title: Stretched_NRVMs_control_rep_01


title: CSM5FZ1G


title: Pho4 replicate 2 GFP control


title: Healthy control 97

status: Public on Mar 16 2018

city: Lørenskog

first: Vegard

last: Wyller

address: Sykehusveien 20

country: Norway

institute: Akershus University Hospital

data_processing:
FastQC for removing of low quality reads and adapters
Reads were mapped to the human genome version GRCh38.p2 by STAR
Gene expression abundance was quantified by the Subread package at the gene level
Normalization of read quantification and removal of variation following RUVg method
Differentially expressed genes between CFS patients and controls were identified using DESeq2 package
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: Tab delimited file of counts

source_name: Whole Blood

extract_protocol:
Invitrogen Tempus stabilizing reagents (Applied Biosystems, Thermo Fischer Scientific, Waltham, MA, USA)
HiSeq 2500 Illumina protocol for 101 bp single-end strand-specific sequencing

treatment_protocol: 28 patients and 19 controls

tag: condition

value: healthy


title: Healthy control 90


title: Healthy control 72


title: Healthy control 414


title: Healthy control 235


title: Healthy control 44


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML48

type: genomic

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

description: single experiment

hyb_protocol: Comparative MCIp hybridizations on CpG island oligonucleotide microarrays (Agilent) were performed using the recommended, stringent protocol (Agilent).

scan_protocol: Scanned on an Agilent scanner at 5 µm resolution. Images were analysed and data extracted using Agilent Feature Extraction Software (version 9.5.1).

data_processing:
Linear normalized, background subtracted VALUE data were obtained from log10 transformed, processed Red signal/processed Green signal values derived from image analysis with Agilent Feature Extraction Software (version 9.5.1).  Processed signal intensities were further normalized using GC-dependent regression and imported into Microsoft Office Excel 2007 for further analysis.
normalized signal intensities for cancer and normal cells; log10 ratio (Alexa Fluor 5–dCTP/Alexa Fluor3–dCTP) representing cancer MCIp/ normal MCIp; and average signal intesity of both channels;

label: Alexa Fluor 5–dCTP

source_name: acute myeloid leukemia

label_protocol: Enriched methylated DNA fragments of the high-salt MCIp fractions were labeled with Alexa Fluor 5–dCTP (cancer cells) and Alexa Fluor 3–dCTP (normal cells) using the BioPrime Total Genomic Labeling System (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

growth_protocol: Leukemic blasts and bone marrow cells from AML patients were collected during routine diagnostic bone marrow aspirations. Patients had given informed consent to additional sample collection and analyses according to a protocol approved by the local ethical committee. DNA was prepared after Ficoll gradient centrifugation using Qiagen Blood & Cell Culture DNA Kit. DNA concentration was determined with the NanoDrop spectrophotometer and quality was assessed by agarose gel electrophoresis.

extract_protocol: MCIp enrichment of methylated DNA was performed essentially as described (Gebhard et al. 2006, Cancer Research). In brief, genomic DNA was sonicated to a mean fragment size of 350-400 bp. Two µg of each sample were incubated with 150 µl Protein A-Sepharose 4 Fast Flow beads (GE Healthcare) coated with 60 µg purified MBD-Fc protein in 2 ml Ultrafree-MC centrifugal filter devices (Amicon/Millipore) for 3 h at 4°C in buffer containing 300 mM NaCl. Beads were centrifuged to recover unbound DNA fragments (300 mM fraction) and subsequently washed with buffers containing increasing NaCl concentrations (400, 500, 550 mM). Densely CpG-methylated DNA was eluted with a high-salt buffer (1000 mM NaCl) and all fractions were desalted using the MinElute PCR purification kit (Qiagen). The separation of CpG methylation densities of individual MCIp fractions was controlled by qPCR using primers covering the imprinted SNRPN

tag: dissease state

value: human acute myeloid leukemia

value: female

tag: fab

value: cancer cells

tag: protocol

value: MCIp enrichment

label: Alexa Fluor 3–dCTP

source_name: peripheral blood monocytes

value: male

value: peripheral blood monocytes; mixture of three young (age 20-30) and healthy donors


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML51

description: single experiment


title: Healthy control 449


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML60

description: single experiment


title: Healthy control 189


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML44

description: single experiment


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML63

description: single experiment

value: RAEB-T


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML66

description: single experiment


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML47

description: single experiment


title: Healthy control 188


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML61

description: single experiment


title: Healthy control 169


title: Healthy control 168


title: Healthy control 178


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML58

description: single experiment


title: Healthy control 153


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML65

description: single experiment


title: Healthy control 142


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML46

description: single experiment


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML56

description: single experiment


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML50

description: single experiment


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML57

description: single experiment


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML49

description: single experiment


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML43

description: single experiment


title: Healthy control 110


title: Healthy control 139


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML37

description: single experiment


title: Healthy control 96


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML54

description: single experiment


title: Healthy control 121


title: Patient 73

value: CFS


title: Patient 79


title: Patient 433


title: Patient 461


title: Patient 454


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML36

description: single experiment


title: Patient 431


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML59

description: single experiment


title: Patient 435


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML45

description: single experiment


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML55

description: single experiment


title: Patient 467


title: Patient 416


title: Patient 406


title: Patient 391


title: Patient 387


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML42

description: single experiment


title: Patient 36


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML38

description: single experiment


title: Patient 388


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML52

description: single experiment


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML62

description: single experiment


title: Patient 368


title: Comparative MCIp-on-Chip for akute myeloid leukemia and human blood monocytes AML40

description: single experiment


title: Patient 339


title: Patient 276


title: Healthy control 108


title: Patient 242


title: Patient 245


title: Patient 266


title: Patient 220


title: Patient 211


title: Patient 116


title: Patient 274


title: Patient 87


title: Patient 147


title: Patient 118


title: Patient 100


title: P8a_4.18.13

city: Berkeley

first: Yvette

middle: M

last: Piceno

address: 1 Cyclotron Rd., MS 70A-3317

department: Ecology

institute: LBNL

hyb_protocol: Arrays were hybridized overnight at 48degC and 60 rpm and then washed and stained using standard Affymetrix buffers/reagents.

scan_protocol: Images were captured on an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
CEL files were converted to CELa files and then processed using proprietary software (PhyCA). Data processing performed by Second Genome (http://www.secondgenome.com/platform/services/).
Data are provided as binary or intensity values scaled to internal standards. See README_PhyloChip_FMF-probiotics_Pepoyan.txt on series record. The data file GSE111835_MIAME_Phylochip_data_FMF-probiotics_Pepoyan.txt includes species taxonmy, OTU_ID, GenBank accession ID (GB_ACC) and gg_ID.

organism: human gut metagenome

source_name: Patient

label_protocol: TDT enzyme (P/N PM1875; Promega; Madison, WI) and GeneChip Labeling Reagent (P/N 90042; Affymetrix; Santa Clara, CA) were used to label fragmented amplicons.

extract_protocol: The ZR Fecal DNA MiniPrep (ZYMO RESEARCH) and the UltraClean® Tissue & Cells DNA Isolation Kit (MoBIO) both were used for total genomic DNA isolation from each sample following the manufacturers’ recommendations. An equal amount of genomic DNA from each extract was combined for a given stool sample prior to 16S rRNA gene amplification for microarrays.

treatment_protocol: see publication

tag: subject id

tag: human donor diagnosis

value: Familial Mediterranean fever

tag: tissue source of metagenome

value: human feces

tag: Sex

value: Male

value: Placebo

tag: timepoint

value: pre-treatment

tag: replicate

value: yes


title: P7c_5.09.13

tag: treatment

value: Narine

value: no


title: P9a_5.09.13

value: Colibacteron


title: P7a_4.23.13


title: P7b_4.18.13

value: post-treatment


title: P6b_4.19.13


title: P6c_5.09.13


title: P9b_4.18.13


title: P8b_4.18.13


title: P6a_4.19.13


title: HK3

city: Tianshui

first: Fang

last: Ma

state: Qinzhou District

address: South Xihe Road

department: College of Bioengineering and Technology

institute: Tianshui normal university

data_processing:
raw reads data were firstly trimmed off low quality reads and adaptor sequence through custom perl and python scripts to obtain clean reads. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, the reads with high sequencing quality and ranging from 18–35nt in length were annotated by searching against the GenBank database and the Rfam database. In addition, the small RNA tags of rainbow trout were mapped and aligned to the rainbow trout genome (https://www.genoscope.cns.fr/trout/) by Bowtie without mismatch to analyze their expression and distribution on the reference
Small RNA tags were mapped to RepeatMasker, Rfam database or rainbow trout mRNAs to remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA. Mapped small RNA tags were used to looking for known miRNA by miRBase20.0 as reference.
Mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures
miRNAs expression levels between the control and treated groups, read counts for each identified miRNA were estimated by TPM (transcript per million)
Target genes of miRNAs were predicted using miRanda program
The novel_nnnn is a newly discovered miRNA in our sequencing data, without naming. A total of 989 novel miRNAs were identified, which may be unique to rainbow trout (Oncorhynchus mykiss). We have uploaded the FASTA file of mature sequence and hairpin sequence of 989 novel miRNA.
Genome_build: (https://www.genoscope.cns.fr/trout/
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Oncorhynchus mykiss

source_name: head kidney of f rainbow trout

extract_protocol:
Total RNA of the six libraries  was extracted using the standard TRIzol™. Agarose gel electrophoresis, Nano Photometer® Spectrophotometer and Bioanalyzer 2100 System  were  employed to evaluate the quantity and quality of the total RNAs.
About 3 μg total RNA from each sample was used  to construct small RNA library. Six sequencing libraries were generated using the NEBNext® Multiplex small RNA Library Prep Kit for Illumina®

tag: tissue

value: head kidney

value: 1 year

value: female

tag: group

value: heat-treated group


title: CK1

value: control group


title: CK3


title: HK1


title: P5c_5.09.13


title: CK2


title: P5a_4.19.13


title: P52c_5.09.13


title: P52b_4.23.13


title: P51b_4.19.13


title: P52a_4.18.13


title: HK2


title: P51a_4.19.13


title: P4b_4.18.13


title: HuTconvFroz

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
mapping with tophat2 on the Hg19 transcriptome
filtering out low alignment score reads and multiple mapping reads (samtools)
duplication filtering using unique molecular identifiers (custom scripts)
Genome_build: Hg19
Raw sequence data is unavailable due to patient privacy concerns
Supplementary_files_format_and_content: raw read counts

source_name: PBMC

growth_protocol: Live cells were sorted by flow cytometry from the human peripheral blood.

extract_protocol:
Peripheral mononuclear cells were isolated by Ficoll gradient. Treg cells were sorted by flow cytometry as DAPI- TCRb+ CD4+ CD25+ CD127low cells, Tconv cells as DAPI- TCRb+ CD4+ CD25- CD127high cells. Single cells were then encapsulated in nanodroplets according to the InDrops protocol.
mRNA was reverse transcribed using adapters containing oligo dT in each droplet. The emulsion was then broken and linear amplification was performed by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a NextSeq500.

tag: library name

value: Tconv

tag: sample type

value: HuTconvFroz

tag: age (months)

value: PBMC


title: HuTconvFresh

description: Raw sequence data is unavailable due to patient privacy concerns

tag: cell type

value: HuTconvFresh

value: male


title: HuTregFroz

value: Treg

value: HuTregFroz


title: HuTregFresh

value: HuTregFresh


title: P49b_4.19.13

value: Familial Mediterranean fever

value: human feces

value: Male

value: Placebo

value: yes


title: P49a_4.19.13

value: pre-treatment


title: P46b_5.09.13

value: Narine

value: post-treatment


title: P5b_4.19.13


title: P4a_4.18.13

value: Colibacteron


title: P47a_4.18.13


title: P48b_5.09.13


title: P46a_5.09.13


title: P47b_4.18.13


title: P48a_4.18.13


title: P44a_4.18.13

value: Female


title: P45a_4.18.13


title: P42b_4.19.13


title: P45b_4.18.13


title: P44b_4.18.13


title: P43a_4.19.13


title: P42a_5.09.13


title: P43b_4.19.13


title: P41b_4.19.13


title: P40b_4.18.13

value: no


title: P3a_4.18.13


title: P40a_4.18.13


title: P3b_4.18.13


title: P45c_5.09.13


title: P39b_4.18.13


title: P38a_5.09.13


title: P36c_5.09.13


title: P39a_4.18.13


title: P36b_5.09.13


title: P35c_5.09.13


title: P35b_4.19.13


title: P38b_4.18.13


title: P37a_4.19.13


title: P33b_4.19.13


title: P36a_4.18.13


title: P37b_4.19.13


title: P34a_4.18.13


title: P34c_5.09.13


title: P34b_4.18.13


title: P2a_5.09.13


title: P2c_5.09.13


title: P31b_4.18.13


title: P31a_4.18.13


title: P41a_4.19.13


title: P29a_4.18.13


title: P27b_4.18.13


title: P35a_4.19.13


title: P2b_4.19.13


title: P29b_5.09.13


title: P25b_5.09.13


title: P27a_4.18.13


title: P33a_4.19.13


title: P25c_5.09.13


title: P25a_4.18.13


title: P24a_4.18.13


title: P24b_4.18.13


title: P23b_4.19.13


title: P23a_5.09.13


title: P22a_4.19.13


title: P21b_4.18.13


title: P1b_4.19.13


title: P21a_5.09.13


title: P22c_5.09.13


title: P1c_5.09.13


title: P22b_4.19.13


title: P19b_4.19.13


title: P18c_5.09.13


title: P1a_4.19.13


title: P19a_4.23.13


title: P16b_4.18.13


title: P18b_4.19.13


title: P17b_4.19.13


title: P13b_4.19.13


title: P17c_5.09.13


title: P18a_4.19.13


title: P17a_4.19.13


title: P14b_4.19.13


title: P13a_4.19.13


title: P14a_4.19.13


title: P12a_4.18.13


title: P12b_4.18.13


title: P11a_4.18.13


title: P11b_4.18.13


title: P10c_5.09.13


title: P10b_4.18.13


title: H9b_4.23.13

source_name: Healthy volunteer

value: Healthy volunteer


title: H9a_4.23.13


title: P10a_4.18.13


title: H8a_4.23.13


title: P16a_5.09.13


title: H7b_4.24.13


title: H6b_4.19.13


title: H4b_4.23.13


title: H5a_4.24.13


title: Control CD4+T cell 5

city: Chang Sha

first: jingjiao

last: chen

state: Hu Nan

address: Renmin

institute: xiangya hospital

description: Biological replicate 5 of 6. Control.from healthy people.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

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 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CD4 +T cells of control

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: Total RNA extracted using Trizol following manufacturer's instructions

tag: disease state

value: normal

value: CD4+ T cells

value: Peripheral Blood

tag: age

tag: gender

value: female


title: Control CD4+T cell 4

description: Biological replicate 4 of 6. Control.from healthy people.

value: male


title: MG CD4+T cell 1

description: Biological replicate 1 of 6.experimental group.from patients with MG.

source_name: CD4 +T cells of patients with MG

value: myasthenia gravis


title: Control CD4+T cell 3

description: Biological replicate 3 of 6. Control.from healthy people.


title: MG CD4+T cell 3

description: Biological replicate 3 of 6.experimental group.from patients with MG.


title: MG CD4+T cell 5

description: Biological replicate 5 of 6.experimental group.from patients with MG.


title: H3a_4.19.13

value: human feces


title: H30b_4.24.13


title: Control CD4+T cell 1

description: Biological replicate 1 of 6. Control.from healthy people.


title: H2b_4.23.13


title: H8b_4.23.13


title: H30a_4.24.13


title: MG CD4+T cell 6

description: Biological replicate 7 of 6.experimental group.from patients with MG.


title: MG CD4+T cell 4

description: Biological replicate 4 of 6.experimental group.from patients with MG.


title: MG CD4+T cell 2

description: Biological replicate 2 of 6.experimental group.from patients with MG.


title: H7a_5.09.13


title: H2a_4.23.13


title: H5b_4.24.13

value: Male


title: H6a_4.19.13


title: input, rep 1, veh (Pol2)

first: Kelsey

last: Tyssowski

address: 77 Ave Louis Pasteur

department: Genetics

description: Sample 51

data_processing:
Base-calling with Illumina RTA v2 (default NextSeq settings)
Alignment was done using bowtie2.
Resulting SAM files were converted to BAM files then to BED files using samtools and bedtools, with reads extended to 300 base pairs
BED files were then converted to bedgraphs using bedtools and then to bigWigs using UCSC-tools, reads were assigned to individual enhancers or promoters using bedtools map
Data was normalized as specificed (either by input, control region, or read depth).
Genome_build: mm9
Supplementary_files_format_and_content: Excel files with input-normalized and control-region-normalized values for regions of interest.
BigWig files normalized for read-depth (H3K27ac) or to control regions (Pol2)

source_name: Primary Culture Mouse Neurons

extract_protocol:
Neurons were fixed in 1% formaldehyde and lysed in 10 mM Tris pH 8.0, 1mM EDTA, 1 mM EGTA, 1X Roche complete EDTA-free protease inhibitors, 0.15% SDS. Chromatin was sonicated and immunoprecipitaed, as described in the methods section of  the accompanying publication (Tyssowski et al., 2018).
Libraries were prepared using 5ug of immunoprecipitated DNA or input DNA with the NuGen Ultralow V2 1-96 library prep kit.

tag: mouse strain

tag: time point

tag: drug

value: DMSO

tag: chip antibody


title: input, rep 2, U0126 (Pol2)

description: Sample 52


title: H4a_4.23.13

tag: subject id

tag: human donor diagnosis

tag: tissue source of metagenome

tag: Sex

value: yes


title: H29b_4.23.13

tag: treatment

value: Placebo

tag: timepoint

tag: replicate


title: 360m, rep 2, U0126, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 50

value: anti-RNAPol2, abcam, ab817


title: Control CD4+T cell 6

description: Biological replicate 6 of 6. Control.from healthy people.

tag: tissue


title: H28a_4.23.13

value: Narine

value: pre-treatment


title: H29a_4.23.13

value: Female


title: H28b_4.23.13

value: post-treatment


title: 360m, rep 1, U0126, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 49


title: Control CD4+T cell 2

description: Biological replicate 2 of 6. Control.from healthy people.


title: 360m, rep 2, veh, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 48


title: 360m, rep 1, veh, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 47


title: H27a_4.24.13

value: Healthy volunteer


title: H27b_4.24.13


title: 180m, rep 1, U0126, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 46


title: 180m, rep 2, veh, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 45


title: 180m, rep 1, veh, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 44


title: H3b_4.19.13


title: H26b_4.24.13


title: 60m, rep 2, U0126, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 43


title: H26a_4.24.13


title: H25b_5.09.13


title: 60m, rep 1, U0126, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 42


title: 60m, rep 2, veh, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 41


title: H25a_4.24.13


title: H24a_4.23.13


title: H24b_4.23.13


title: 60m, rep 1, veh, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 40


title: 30m, rep 2, U0126, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 39


title: H23b_4.23.13


title: H22b_4.24.13


title: H23a_4.23.13


title: H22a_5.09.13


title: 30m, rep 2, veh, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 37


title: 30m, rep 1, veh, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 36