title: AD, CBL sample 07--34

description:
Alzheimer's CBL sample
CBL 07--34

source_name: CBL sample 07--34

tag: brain region


title: C4-2 PXNsiRNA_DHT3

status: Public on Aug 01 2019

type: SRA

city: Rochester

first: Stephen

middle: R

last: Hammes

state: NY

address: 601 Elmwood Ave, Box 693

department: Medicine

country: USA

institute: University of Rochester

description:
LNCaP derived castration resistant prostate cancer cell line
Transfected with paxillin targeted siRNAfor 48 hours, serum starved for 12 hours and treated with 2.5nM Dihydrotestosterone(DHT) for 24 hours

library_source: transcriptomic

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15
Genome Alignment - STAR_2.5.2b, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - subread-1.5.0p3, featurecounts, -s 2 -t exon -g gene_name
Genome_build: GRCh38 + gencode 25
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: prostate cancer cell line

growth_protocol: C4-2 cells was growing in RPMI 1640 media supplied with 10% FBS and 1% penicillin and strepavidin.

extract_protocol:
mRNA was isolated using Qiagen Rneasy Plus Mini Kit
Illumina TruSeq Stranded mRNA

treatment_protocol: C4-2 cells were transfected with either Non-specific siRNA or Paxillin-targeted siRNA for 48 hours, followed by serums starvation of 12 hours, cells are then treated with either 2.5nM dihydrotestosterone (DHT) or vehicle (ethanol)

tag: cell type

tag: transfection

value: paxillin targeted siRNA

tag: treatment

value: 2.5nM Dihydrotestosterone(DHT)


title: 4c Hepatocytes [Hep_4c_160]

type: RNA

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
Expression levels were normalized with Actb.
A -deltaCt value normazized to Actb is used as a gene expression level for each gene.

label: FAM

organism: Rattus norvegicus

source_name: Percoll-treated and FACS-sorted 4c hepatocytes

label_protocol: Single cell capture, lysis and RT pre-amplification experiments were performed using C1 Auto Prep System (Fluidigm) according to the manufacturer's instructions. After lysis, reverse-transcription (25 °C for 10 min, 42 °C for 60 min, 85 °C for 5 min) and pre-amplification for 18 cycles (each cycle: 95 °C for 15 sec, 60 °C for 4 min), single-cell cDNA was harvested, transferred to a 96-well plate and diluted 6 times with cDNA dilution buffer. After lysis, reverse-transcription (25 °C for 10 min, 42 °C for 60 min, 85 °C for 5 min) and pre-amplification for 18 cycles (each cycle: 95 °C for 15 sec, 60 °C for 4 min), single-cell cDNA was harvested, transferred to a 96-well plate and diluted 6 times with cDNA dilution buffer.

extract_protocol: Adult hepatocytes were isolated from Wistar rats by two-step collagenase perfusion. NPCs were harvested from the undigested remnant tissue by further digestiong with collagenase-hyaluronidase.

tag: strain

value: Wistar

tag: age

value: 6 week old

tag: Sex

value: Female


title: PC3 NSPsiRNA_1

description:
Androgen Receptor negative bone metastasis derived prostate cancer cell line
Transfected with Non-specific siRNAfor 72 hours, replicate 1
2a

data_processing:
Data Formatting - bcltofastq-1.8.4
CLEANING - seqclean-x86_64 (seqclean & cln2qual), fastqc-0.10.1, fastx_toolkit_0.0.13 (fastq_quality_trimmer)
MAPPING - SHRiMP_2_2_3
DIFFERENTIAL EXP. - cufflinks-2.0.2.Linux_x86_64 (cuffdiff2)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw count and FPKM values for each sample

growth_protocol: PC3 cells was growing in RPMI 1640 media supplied with 10% FBS and 1% penicillin and strepavidin.

extract_protocol:
mRNA was isolated using Qiagen Rneasy Plus Mini Kit
Illumina TruSeq mRNA

treatment_protocol: PC3 cells were transfected with either Non-specific siRNA or Paxillin-targeted siRNA for  72 hours

tag: cell line

value: non-specific siRNA


title: 4c Hepatocytes [Hep_4c_159]


title: AD, CBL sample 04--09

type: genomic

city: Tempe

first: Danielle

middle: Lisa

last: Brokaw

state: AZ

address: Biodesign Institute Building C, 1001 S McAllister Ave

department: Center for Neurodegeneration, Biodesign

institute: Arizona State University

description:
Alzheimer's CBL sample
CBL 04--09

hyb_protocol: Samples were randomly assigned to one of nine Illumina 450K plates and hybridized according to protocol.

scan_protocol: iScan System according to user protocol

data_processing:
Data was analyzed in R (version 3.4.2) using minfi (1.23.4) and SVA (3.26.0). Poorly performing probes (detection p-value < 0.05) and sex chromosome probes were removed from the analysis. NOOB and functional normalization were performed using the minfi package according author guidelines. Confounding variables were detected using SVA and, alongside batch/plate effects, were accounted for using the ComBat algorithm.
Normalized Average betas included as supplementary files (processedSamples*.txt) on the Series record.
Methylated and unmethylated signal intensities included as supplementary files (signalIntensities*.txt) on the Series record.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: CBL sample 04--09

label_protocol: Standard Illumina Protocol

extract_protocol: Tissue was incubated in lysis buffer (100 mM Tris HCL pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl, 100 ug/mL Proteinase K) overnight at 55°C.  and disassembled using a pestle. Disassociated tissue was treated with 4 uL of Rnase A for 30 minutes at RT and then treated with ethanol overnight at -20°C. 1 ug of extracted DNA per sample was treated with bisulfite and used in the assay.

tag: plate

tag: bead chip

tag: well position

tag: tissue

value: brain

value: CBL

tag: gender

value: F

tag: diagnosis

value: AD


title: AD, CBL sample 01--48

description:
Alzheimer's CBL sample
CBL 01--48

source_name: CBL sample 01--48


title: 4c Hepatocytes [Hep_4c_158]


title: C4-2 PXNsiRNA_DHT2


title: 4c Hepatocytes [Hep_4c_162]


title: AD, CBL sample 97--18

description:
Alzheimer's CBL sample
CBL 97--18

source_name: CBL sample 97--18


title: AD, CBL sample 97--16

description:
Alzheimer's CBL sample
CBL 97--16

source_name: CBL sample 97--16


title: C4-2 PXNsiRNA_DHT1


title: 4c Hepatocytes [Hep_4c_157]


title: 4c Hepatocytes [Hep_4c_156]


title: AD, CBL sample 93--32

description:
Alzheimer's CBL sample
CBL 93--32

source_name: CBL sample 93--32


title: C4-2 PXNsiRNA_Ctrl3

description:
LNCaP derived castration resistant prostate cancer cell line
Transfected with paxillin targeted siRNAfor 48 hours, serum starved for 12 hours and treated with vehicle (ethanol) for 24 hours

value: vehicle


title: C4-2 PXNsiRNA_Ctrl2


title: AD, CBL sample 97--29

description:
Alzheimer's CBL sample
CBL 97--29

source_name: CBL sample 97--29


title: 4c Hepatocytes [Hep_4c_155]


title: C4-2 PXNsiRNA_Ctrl1


title: AD, CBL sample 95--01

description:
Alzheimer's CBL sample
CBL 95--01

source_name: CBL sample 95--01


title: 11_WF

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Gene expression data from LnCap cell line

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized by the Affymetrix Human Gene 2.1 ST ArrayStrip (20 h, 48 ◦C).

scan_protocol: After the hybridization, the microarrays were washed and stained according to the technical protocol by means of the Affymetrix GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA, USA). The array strips were scanned on Imaging Station of GeneAtlas System (ThermoFisher Scientific, Waltham, MA, USA).

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

label: biotin

source_name: MDA-MB-468 cells incubated with 10% of WF surgical wound fluid

label_protocol: Total RNA (100 ng) from each sample was subjected to two rounds of sense cDNA amplification, biotin labelling and cDNA fragmentation using the GeneChip Whole Transcript (WT) PLUS Reagent Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Cells were cultured in a humidified atmosphere with 5% carbon dioxide at 37°C in Dulbecco modified Eagle medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin 10,000 U/ml .

extract_protocol: Total RNA was purified using Direct-zol™ RNA MiniPrep (Zymo Research; Irvine, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Shortly, MDA-MB-468 cells were irradiated in suspension. A total dose of 10 Gy was administered at approximately 2.5 Gy/min using GammaCell® 1000 Elite (BestTheratronics Ltd, Canada) using a Caesium-137 source. After irradiation, the cells were cultured for 24h and then the RIBE medium was collected, sterile-filtered, and stored at − 80 °C. MDA-MB-468 cells were incubated with SWF obtained from the two study groups (RT-WF and WF groups). In all cases, the wound fluid was conditioned in DMEM without fetal bovine serum (FBS). The WF and RT-WF groups both contained 10% WF, which were conditioned in DMEM without FBS, as stated above. A third group of cells was conditioned in 5% RIBE and 5% WF (WF+RIBE).

value: human breast cancer cell line


title: 15_WF+RIBE

source_name: MDA-MB-468 cells incubated with 5% of WF surgical wound fluid and 5% of RIBE medium


title: 4c Hepatocytes [Hep_4c_154]


title: C4-2 NSPsiRNA_DHT3

description:
LNCaP derived castration resistant prostate cancer cell line
Transfected with Non-specific siRNAfor 48 hours, serum starved for 12 hours and treated with 2.5nM Dihydrotestosterone(DHT) for 24 hours


title: 10_WF


title: 4c Hepatocytes [Hep_4c_153]


title: AD, CBL sample 96--31

description:
Alzheimer's CBL sample
CBL 96--31

source_name: CBL sample 96--31

value: M


title: C4-2 NSPsiRNA_DHT2


title: 08_RT-WF

source_name: MDA-MB-468 cells incubated with 10% of RT-WF surgical wound fluid


title: 14_WF+RIBE


title: AD, CBL sample 96--29

description:
Alzheimer's CBL sample
CBL 96--29

source_name: CBL sample 96--29


title: 13_WF+RIBE


title: 12_WF


title: 07_RT-WF


title: 06_RIBE

source_name: MDA-MB-468 cells incubated with 10% of RIBE medium


title: 4c Hepatocytes [Hep_4c_152]


title: 05_RIBE


title: C4-2 NSPsiRNA_DHT1


title: AD, CBL sample 07--06

description:
Alzheimer's CBL sample
CBL 07--06

source_name: CBL sample 07--06


title: AD, CBL sample 05--58

description:
Alzheimer's CBL sample
CBL 05--58

source_name: CBL sample 05--58


title: C4-2 NSPsiRNA_Ctrl1

description:
LNCaP derived castration resistant prostate cancer cell line
Transfected with Non-specific siRNAfor 48 hours, serum starved for 12 hours and treated with vehicle (ethanol) for 24 hours

source_name: prostate cancer cell line


title: AD, CBL sample 05--52

description:
Alzheimer's CBL sample
CBL 05--52

source_name: CBL sample 05--52


title: C4-2 NSPsiRNA_Ctrl3


title: AD, CBL sample 05--11

description:
Alzheimer's CBL sample
CBL 05--11

source_name: CBL sample 05--11


title: 4c Hepatocytes [Hep_4c_150]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes


title: 04_RIBE


title: 09_RT-WF


title: 03_CTR

source_name: MDA-MB-468 cell line served as control


title: AD, CBL sample 06--28

description:
Alzheimer's CBL sample
CBL 06--28

source_name: CBL sample 06--28


title: LNCaP PXNsiRNA_DHT3

description:
Lymph node derived androgen sensitive prostate cancer cell line
Transfected with paxillin targeted siRNA for 48 hours, serum starved for 12 hours and treated with 2.5nM Dihydrotestosterone(DHT) for 24 hours replicate 3

data_processing:
Data Formatting - bcltofastq-1.8.4
Data Cleaning - Trimmomatic-0.32, SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15
Genome Alignment - STAR_2.4.2a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - subread-1.5.0p3, featurecounts, -s 2 -t exon -g gene_name
Genome_build: GRCh38 + gencode 23
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

growth_protocol: LNCaP cells was growing in RPMI 1640 media supplied with 10% FBS and 1% penicillin and strepavidin.

treatment_protocol: LNCaP cells were transfected with either Non-specific siRNA or Paxillin-targeted siRNA for 48 hours, followed by serums starvation of 12 hours, cells are then treated with either 2.5nM dihydrotestosterone (DHT) or vehicle (ethanol)

value: LNCaP


title: 4c Hepatocytes [Hep_4c_146]


title: C4-2 NSPsiRNA_Ctrl2


title: 01_CTR


title: 4c Hepatocytes [Hep_4c_149]


title: 4c Hepatocytes [Hep_4c_148]


title: 4c Hepatocytes [Hep_4c_151]


title: LNCaP PXNsiRNA_DHT1

description:
Lymph node derived androgen sensitive prostate cancer cell line
Transfected with paxillin targeted siRNA for 48 hours, serum starved for 12 hours and treated with 2.5nM Dihydrotestosterone(DHT) for 24 hours replicate 1


title: AD, CBL sample 05--19

description:
Alzheimer's CBL sample
CBL 05--19

source_name: CBL sample 05--19


title: 02_CTR


title: LS_degradome

city: Wuhan

first: li

last: chen

address: Huazhong Agricultural University

country: China

institute: National Key Laboratory of Crop Genetic Improvement

description:
degradome sequencing
LS.txt.xlsx

data_processing:
Sequenced reads were trimmed for adaptor sequence, abandon seqences small than 18 nt, and masked for low-complexity or low-quality sequence, then mapped to ref2 database using soap -v 0 -r 2 -s 7 -p 7 -a clean.fa -d ref_genome.fa -o match_genome.soap
The secondary hairpin structures were predicted using Mireap with the following parameters: a hairpin structure with a free energy less than –18 kcal mol–1, the spacebetween miRNA and miRNA* is less than 300 nt, the candidates have more than 16 matched nucleotides and fewer than 4 nucleotide bulges between miRNA and miRNA*, and the minimal folding free energy index (MFEI) values are more than 0.85
The filtered reads were then mapped to the B. napus cDNA to potential miRNA target sites, identified using the TargetFinder v1.6 script, using an updated version of the CleaveLand pipeline v3.0.1. The height of the degradome peak at each position is placed into one of five categories, described below. The Categories 0−3 have more than 1 raw reads at the position. Category 0: there is only one single maximum on the transcript; Category 1: there is more than one maximum position on the transcript and expressed equally; Category 2: abundance at position is less than maximum but higher than the median of the transcript; Category 3: abundance at position is equal to or less than the median of the transcript; Category 4 has only 1 raw read at the position.
Genome_build: Brassica napus genome (http://www.genoscope.cns.fr/brassicanapus/data/Brassica_napus_v4.1.chromosomes.fa.gz) and mirBase version 21.0
Supplementary_files_format_and_content: Supplementary_files_format_and_content: abundance: length abundance sequence. FASTA files with novel miRNA sequences are available on the series record.

organism: Brassica napus

source_name: fruit

growth_protocol: Populations of backcross progenies with long siliques and short siliques (LS and SS), derived from the cross of 8008 × 4942, were created grown in an experimental field at the Huazhong Agricultural University (Wuhan, Hubei Province, China).

extract_protocol:
Pistils/siliques from LS and SS lines were harvested at 0–7 days after pollination (DAP). When the flower was opened, pistils were harvested (0 DAP). Then, inflorescences were labeled to harvest siliques of defined stages. Each stage was harvested from ~12 plants, directly frozen in liquid nitrogen, and stored at −80°C. Total RNA was extracted by using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The tissue samples used in RNA extraction were collected from two replicated experiments.
sRNA library construction and deep sequencing were performed as described previously. Briefly, small RNAs with 18–30-nt long small RNAs were purified from 10 µg of total RNA in a 15% polyacrylamide gel by electrophoresis and ligated to 5′and 3′ RNA adaptors. The purified RNAs were transcribed into cDNA, followed by PCR amplification to generate the DNA pool. Finally, 4 libraries were sequenced on an Illumina Genome Analyzer at the Beijing Genomics Institute (BGI, Shenzhen, China). Degradome libraries were constructed as previously described. Approximately 200 ug of total RNA was used for the purification of polyadenylated RNA molecules using the Oligotex mRMA kit (Qiagen, Valencia, CA, USA). Then, using T4 RNA ligase (Ambion, USA) ligated the adaptor to the cleaved products which have a 5′-monophosphate at the 5′ end. The ligated products were purified and amplified by five PCR cycles for reverse transcription reaction, then digested with MmeI and ligated to a 3′ double DNA adaptor. Finally, another 20 cycles of PCR were amplified, gel-purified PCR products were sequenced on Illumina Genome Analyser.

value: silique

tag: developmental stage

value: 0-7days after pollination


title: SS_degradome

description:
degradome sequencing
SS.txt.xlsx


title: LNCaP PXNsiRNA_DHT2

description:
Lymph node derived androgen sensitive prostate cancer cell line
Transfected with paxillin targeted siRNA for 48 hours, serum starved for 12 hours and treated with 2.5nM Dihydrotestosterone(DHT) for 24 hours replicate 2


title: 4c Hepatocytes [Hep_4c_147]


title: 4c Hepatocytes [Hep_4c_145]


title: AD, CBL sample 98--30

description:
Alzheimer's CBL sample
CBL 98--30

source_name: CBL sample 98--30


title: LS-1_smallRNA-seq

description:
small RNA sequencing
LS-1_vs_SS-1_known_miRNADiffExp.Expdiff.dat.txt
LS-1_vs_SS-1_novel_miRNADiffExp.Expdiff.dat.txt


title: AD, CBL sample 00--50

description:
Alzheimer's CBL sample
CBL 00--50

source_name: CBL sample 00--50


title: SS-1_smallRNA-seq

description:
small RNA sequencing
LS-2_vs_SS-2_known_miRNADiffExp.Expdiff.dat.txt
LS-2_vs_SS-2_novel_miRNADiffExp.Expdiff.dat.txt


title: LNCaP PXNsiRNA_Ctrl3

description:
Lymph node derived androgen sensitive prostate cancer cell line
Transfected with paxillin targeted siRNAfor 48 hours, serum starved for 12 hours and treated with vehicle (ethanol) for 24 hours, replicate 3

value: ethanol for 24 hrs


title: 4c Hepatocytes [Hep_4c_142]


title: LS-2_smallRNA-seq


title: SS-2_smallRNA-seq


title: LNCaP PXNsiRNA_Ctrl2

description:
Lymph node derived androgen sensitive prostate cancer cell line
Transfected with paxillin targeted siRNA for 48 hours, serum starved for 12 hours and treated with vehicle (ethanol) for 24 hours, replicate 2

value: paxillin targeted siRNA


title: 4c Hepatocytes [Hep_4c_143]


title: AD, CBL sample 99--53

description:
Alzheimer's CBL sample
CBL 99--53

source_name: CBL sample 99--53


title: LNCaP PXNsiRNA_Ctrl1

description:
Lymph node derived androgen sensitive prostate cancer cell line
Transfected with paxillin targeted siRNA for 48 hours, serum starved for 12 hours and treated with vehicle (ethanol) for 24 hours, replicate 1


title: 4c Hepatocytes [Hep_4c_141]


title: AD, CBL sample 00--33

description:
Alzheimer's CBL sample
CBL 00--33

source_name: CBL sample 00--33


title: AD, CBL sample 03--19

description:
Alzheimer's CBL sample
CBL 03--19

source_name: CBL sample 03--19


title: HML58-3 treated with OR-2100

city: Tokyo

first: Naoko

last: Hattori

address: 5-1-1 Tsukiji, Chuo-ku

department: Research Institute

country: Japan

institute: National Cancer Center

description:
HML58-3 treated with OR-2100
Sample 4

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: The data were analyzed using GenomeStudio Methylation Module Software (v1.9.0). Beta values were obtained after background correction and normalization to internal controls.

growth_protocol: A derivative cell line of HCT116, HML58-3, was maintained in McCoy's 5A medium with 10% FBS.

extract_protocol: Genomic DNA was extracted using FUJIFILM QuickGene according to standard instructions.

treatment_protocol: Cells were seeded at a density of 3 × 10^5 cells/10-cm dish on Day 0. On Day 1, the medium was replaced with a medium containing 1 µM of drugs, which was freshly dissolved in DMSO and filtered through a 0.2-µ filter. On Day 5, the cells were collected for genomic DNA extraction.


title: 4c Hepatocytes [Hep_4c_140]


title: HML58-3 treated with OR-2003

description:
HML58-3 treated with OR-2003
Sample 3


title: AD, CBL sample 03--01

description:
Alzheimer's CBL sample
CBL 03--01

source_name: CBL sample 03--01


title: HML58-3 treated with mock

description:
HML58-3 treated with mock
Sample 1


title: U1 and RMRP in-cell minusDMS

city: Houston

first: Anthony

middle: M

last: Mustoe

state: TX

address: 1 Baylor Plaza

department: Biochemistry and Molecular Biology

institute: Baylor College of Medicine

description: Sequencing was done in a single batch with 2x150 PE sequencing. U1 and RMRP amplicons share the same sequencing index. Sequences were aligned against U1.fa and RMRP.fa

data_processing:
ShapeMapper (v2.1.4) was used to align and parse mutations from DMS-MaP sequencing data. The --amplicon option was used for amplicon datasets, which masks out primer regions and filters out spurious reads that do not align at the expected 5' and 3' primer sites. The --random-primer-len 9 option was used to mask RT primer sites in randomly primed datasets (16S and 23S rRNAs). The --output-parsed option was used to generate parsed mutation files.
PairMapper (v1.0) was used compute normalized DMS reactivity profiles and identify correlated nucleotides from ShapeMapper-generated parsed mutation files using default parameters.
Genome_build: Sequences used for alignments are noted in SAMPLE description field and are provided as supplementary files

source_name: liquid cell culture

extract_protocol:
Reverse-transcription was performed using specific primers, and DNA libraries were generated using a two-step PCR protocol.
Sample-specific modification and extraction details are provided in the SAMPLES section. All samples were DNase treated and purified using ethanol precipitation prior to reverse transcription.
Mutational profiling (MaP) reverse transcription (RT) was performed using an updated protocol that substantially improves yield and product length. In a 10 μL volume, RNA was mixed with 200 nM specific primer or 20 ng/μL random 9mer and 2 mM dNTPs and incubated at 65 °C for 10 min followed by 4 °C for 2 min. 9 uL 2.22x MaP buffer [1x MaP buffer consists of 6 mM MnCl2, 1 M betaine, 50 mM Tris (pH 8.0), 75 mM KCl, 10 mM DTT] was added and the combined solution incubated at 23 °C for 2 min. Finally, 1 μL SuperScript II Reverse Transcriptase (Invitrogen) was added and the RT reaction was performed according to the following temperature program: 25 °C for 10 min, 42 °C for 90 min, 10x[50 °C for 2 min,  42 °C for 2 min], 72 °C for 10 min. For the adenine riboswitch, ~1 pmol RNA was input into RT. For E. coli and human short RNAs, 0.5-2 μg total RNA was input into RT. For randomly primed E. coli RNA samples (16S and 23S rRNA), 1.5-3 μg total RNA was input into RT. RT products were then purified (Agencourt RNAclean XP beads, Beckman Coulter). Sequencing adaptors were added according to protocols listed in the SAMPLES section.

treatment_protocol: Jurkat cell cultures were supplemented with bicine buffer [200 mM bicine (pH 8.0), final concentration], and treated with 10% ethanol (final vol/vol) for 6 minutes at 37 °C. Total RNA was then extracted using Trizol.

value: Jurkat

tag: probing condition

value: in-cell


title: 4c Hepatocytes [Hep_4c_144]

value: Wistar


title: LNCaP NSPsiRNA_DHT3

description:
Lymph node derived androgen sensitive prostate cancer cell line
Transfected with Non-specific siRNA for 48 hours, serum starved for 12 hours and treated with 2.5nM Dihydrotestosterone(DHT) for 24 hours, replicate 3


title: AD, CBL sample 01--33

description:
Alzheimer's CBL sample
CBL 01--33

source_name: CBL sample 01--33


title: HML58-3 treated with DAC

description:
HML58-3 treated with DAC
Sample 2


title: U1 and RMRP cell-free minusDMS

description: Sequencing was done in a single batch with 2x150 PE sequencing. U1 and RMRP amplicons share the same sequencing index.  fastq files also contain additional reads from unrelated experiments that do not overlap U1 or RMRP. Sequences were aligned against U1.fa and RMRP.fa

treatment_protocol: Total RNA was gently extracted from Jurkat cells, equilibrated in 200 mM bicine (pH 8.0), 200 mM KOAc, 5 mM MgCl2 and treated with 10% ethanol (final vol/vol) for 6 minutes at 37 °C.

value: cell-free


title: 4c Hepatocytes [Hep_4c_139]

value: Female


title: U1 and RMRP  in-cell plusDMS

treatment_protocol: Jurkat cell cultures were supplemented with bicine buffer [200 mM bicine (pH 8.0), final concentration], and modified with 170 mM DMS for 6 minutes at 37 °C. Total RNA was then extracted using Trizol.


title: LNCaP NSPsiRNA_DHT2

description:
Lymph node derived androgen sensitive prostate cancer cell line
Transfected with Non-specific siRNA for 48 hours, serum starved for 12 hours and treated with 2.5nM Dihydrotestosterone(DHT) for 24 hours, replicate 2

value: non-specific siRNA


title: AD, CBL sample 03--02

description:
Alzheimer's CBL sample
CBL 03--02

source_name: CBL sample 03--02

value: brain

value: CBL


title: U1 and RMRP cell-free plusDMS

treatment_protocol: Total RNA was gently extracted from Jurkat cells, equilibrated in 200 mM bicine (pH 8.0), 200 mM KOAc, 5 mM MgCl2 and modified with 170 mM DMS for 6 minutes at 37 °C.


title: LNCaP NSPsiRNA_Ctrl3

description:
Lymph node derived androgen sensitive prostate cancer cell line
Transfected with Non-specific siRNA for 48 hours, serum starved for 12 hours and treated with vehicle (ethanol) for 24 hours, replicate 3

source_name: prostate cancer cell line


title: 4c Hepatocytes [Hep_4c_138]


title: LNCaP NSPsiRNA_DHT1

description:
Lymph node derived androgen sensitive prostate cancer cell line
Transfected with Non-specific siRNA for 48 hours, serum starved for 12 hours and treated with 2.5nM Dihydrotestosterone(DHT) for 24 hours, replicate 1


title: 4c Hepatocytes [Hep_4c_137]


title: LNCaP NSPsiRNA_Ctrl2

description:
Lymph node derived androgen sensitive prostate cancer cell line
Transfected with Non-specific siRNA for 48 hours, serum starved for 12 hours and treated with vehicle (ethanol) for 24 hours, replicate 2


title: LNCaP NSPsiRNA_Ctrl1

description:
Lymph node derived androgen sensitive prostate cancer cell line
Transfected with Non-specific siRNA for 48 hours, serum starved for 12 hours and treated with vehicle (ethanol) for 24 hours, replicate 1


title: AD, CBL sample 07--20

description:
Alzheimer's CBL sample
CBL 07--20

source_name: CBL sample 07--20

value: F

value: AD


title: AD, CBL sample 07--16

description:
Alzheimer's CBL sample
CBL 07--16

source_name: CBL sample 07--16


title: Huh7_Trim71KO_rep3

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

description:
HuH7_Trim71KO_reseq_exon_counts.tab
sample name in processed data file:
K3

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads from mouse samples were aligned to the mm10 genome assembly using the qAlign function from the QuasR R package (v. 1.20.0) with default settings, or using the STAR aligner with the following settings: —outFileterType BySJout, —outFilterMultimapNmax 20, —outMultimapperOrder Random, —outSAMmultNmax 1, —alignSJoverhangMin 8, —alignSJDBoverhangMin 1,  —alignIntronMin 20, —alignIntronMax 1000000
Reads from human samples were aligned to the hg19 genome assembly using the STAR aligner, with the same settings as above.
Gene expression was quantified using Ensembl annotations for mouse and UCSC known Gene annotations for human, downloaded from Bioconductor (“TxDb.Mmusculus.UCSC.mm10.ensGene” and “TxDb.Hsapiens.UCSC.hg19.knownGene”). The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: mm10, hg19
Supplementary_files_format_and_content: Tab-separated: First column contains gene names (Ensembl identifiers), second column contains summed width of exons per gene, following columns contain raw counts of reads overlapping each gene for each sample. HuH7 file: first column contains Entrez IDs, second column contains gene symbols, following columns as in other files.

growth_protocol: Mouse embryonic stem cells (129xC57BL/6 Rosa26Cre-ERT2/BirA-V5 [cMB063 (Ostapcuk et al., 2018)]) were cultured on gelatin-coated dishes in mES medium (DMEM [Gibco; 11995065]) supplemented with 15% fetal bovine serum [Gibco], 1 x non-essential amino acids [Gibco], 1mM sodium pyruvate [Gibco], 2mM L-glutamine [Gibco], 0.1 mM ß-mercaptoethanol [Sigma], 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032], 1x ESGRO® LIF [MerckMillipore; ESG1107]) at 37 °C in 5% CO2.   Ne4C cells (ATCC® CRL-2925™ (Schlett and Madarasz, 1997)) were cultured on poly-l-lysine coated dishes in Ne4C medium (DMEM [Gibco; 11885084] supplemented with 10% fetal bovine serum [Sigma], 2mM L-glutamine [Gibco; 25030081], 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032]) at 37 °C in 5% CO2.   Huh-7 cells (JCRB0403 (Nakabayashi et al., 1982)) were cultured in Huh-7 medium (DMEM [Gibco; 31966021] supplemented with 10% fetal bovine serum [Sigma] 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032]) at 37 °C in 5% CO2.

extract_protocol:
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
TruSeq Illumina Total RNA-seq (stranded - high input)

treatment_protocol: Huh-7 AAVS1EGFP::unc-54unc-54::mab-10condensed/EGFP::unc-54unc-54::mab-10condensed TRIM71 -/-

tag: genotype


title: 4c Hepatocytes [Hep_4c_135]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes


title: DKO ACE-I_HPC 2

city: Leuven

first: Alvaro

last: Cortés Calabuig

address: Herestraat 49 PO box 602

country: Belgium

institute: Genomics Core Leuven

data_processing:
Ea-utils adaptor trimming
Tophat alignment
Htseq-count
Deseq
Genome_build: mm10

organism: Mus musculus

source_name: Heart

growth_protocol: DKO mice were backcrossed for at least 10 generations into the C57BL/6J background, resulting in mice having a 98.4% C57BL/6J background. Homozygous DKO (LDLR-/-;ob/ob) mice were generated using classical intercrossing strategies, for which heterozygous ob/+ and C57BL/6 (WT) mice were purchased from Harlan Laboratory. The mice were genotyped by PCR for LDLR and ob genotype as described before7.

extract_protocol:
Hearts were collected at the age of 24 weeks. Three hearts per group were snap-frozen in liquid nitrogen. Total RNA was extracted using the TRIzol reagent protocol (Invitrogen), purified on an RNeasy spin column (Qiagen), and DNase treated. RNA sample quality was assessed by Nanodrop.
TruSeq Stranded Total RNA

treatment_protocol: LDLR-/-;ob/ob (DKO) and C57Bl6/J (WT) mice were injected with ACE-inhibitor, captopril (10 mg/kg/day) or NaCl 0.9% as controls. Preconditioning (HPC) was induced by five 6-min cycles at 6% oxygen interposed with 6 min at 21% oxygen. Non-preconditioned mice underwent a sham procedure without hypoxia.

value: whole heart

value: post natal 24 weeks

value: LDLR-/- and ob/ob

value: captopril (10 mg/kg/day) + Preconditioning (HPC)


title: Huh7_Trim71KO_rep2

description:
HuH7_Trim71KO_reseq_exon_counts.tab
sample name in processed data file:
K2


title: DKO_HPC 3

value: Preconditioning (HPC)


title: 4c Hepatocytes [Hep_4c_134]


title: DKO_HPC 2


title: DKO ACE-I_HPC 1


title: AD, CBL sample 08--69

description:
Alzheimer's CBL sample
CBL 08--69

source_name: CBL sample 08--69

tag: brain region


title: 4c Hepatocytes [Hep_4c_133]


title: AD, CBL sample 07--54

description:
Alzheimer's CBL sample
CBL 07--54

source_name: CBL sample 07--54


title: DKO_HPC 1


title: AD, CBL sample 01--53

description:
Alzheimer's CBL sample
CBL 01--53

source_name: CBL sample 01--53


title: DKO ACE-I_HPC 3


title: WT ACE-I_HPC 3

value: wild type


title: Huh7_WT_rep3

description:
HuH7_Trim71KO_reseq_exon_counts.tab
sample name in processed data file:
W3

tag: cell type


title: 4c Hepatocytes [Hep_4c_131]


title: 4c Hepatocytes [Hep_4c_136]


title: WT ACE-I_HPC 2


title: 4c Hepatocytes [Hep_4c_132]


title: Huh7_Trim71KO_rep1

description:
HuH7_Trim71KO_reseq_exon_counts.tab
sample name in processed data file:
K1


title: AD, CBL sample 97--07

description:
Alzheimer's CBL sample
CBL 97--07

source_name: CBL sample 97--07


title: AD, CBL sample 02--07

description:
Alzheimer's CBL sample
CBL 02--07

source_name: CBL sample 02--07

value: M


title: Huh7_WT_rep2

description:
HuH7_Trim71KO_reseq_exon_counts.tab
sample name in processed data file:
W2


title: WT ACE-I_HPC 1


title: 4c Hepatocytes [Hep_4c_129]


title: Transgenic cells -NAEK 03_RNA-seq

city: Beijing

first: Yiming

last: Wu

state: Beijing

address: No 38 Xueyuan Road

department: Chemical Bilogy

institute: Peking University Health Science Center

description: in the absent of NAEK

data_processing:
Reads were trimmed for 3' and 5' adaptor
RNA fragments were mapped to the human genome via TopHat2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Genome_build: Homo sapiens genome (GRCh38.87)
Supplementary_files_format_and_content: RPKM of each gene

molecule: polyA RNA

source_name: Transgenic cells

growth_protocol: Transgenic cells were maintained in DMEM medium (Macgene) supplemented with 10% FBS (PAA) at 37 °C in a 5% CO2 incubator.

extract_protocol:
Transgenic cells, either in the present of absent of NAEK (48h), were lysed with Trizol and total RNA was extracted following the manufacturer’s instructions. PolyA+ RNA was selected on oligo(dT) beads (Life Ltd.) and fragmented in Fragmentation Buffer (NEB Ltd.).
RNA fragments were then reverse-transcribed into cDNA and purified on TBE gel. Purified cDNAs were end repaired, ligated with adapters and picked out with a mean size of roughly 200bp. Libraries were built by PCR amplification and further purification by AMPure XP beads.

treatment_protocol: Either in the present or absent of NAEK.

value: Embryonic kidney cells

tag: passsages


title: AD, CBL sample 95--31

description:
Alzheimer's CBL sample
CBL 95--31

source_name: CBL sample 95--31


title: Huh7_WT_rep1

description:
HuH7_Trim71KO_reseq_exon_counts.tab
sample name in processed data file:
W1


title: 4c Hepatocytes [Hep_4c_130]


title: AD, CBL sample 08--06

description:
Alzheimer's CBL sample
CBL 08--06

source_name: CBL sample 08--06


title: WT_HPC 3

tag: treatment


title: 4c Hepatocytes [Hep_4c_128]

tag: strain


title: Transgenic cells -NAEK 02_RNA-seq

description: in the absent of NAEK


title: AD, CBL sample 96--41

description:
Alzheimer's CBL sample
CBL 96--41

source_name: CBL sample 96--41

tag: age


title: 4c Hepatocytes [Hep_4c_127]

tag: Sex


title: Transgenic cells -NAEK 01_RNA-seq

description: in the absent of NAEK


title: WT_HPC 2


title: WT_HPC 1


title: AD, CBL sample 98--12

description:
Alzheimer's CBL sample
CBL 98--12

source_name: CBL sample 98--12


title: AD, CBL sample 97--44

description:
Alzheimer's CBL sample
CBL 97--44

source_name: CBL sample 97--44


title: Transgenic cells +NAEK 03_RNA-seq

description: in the present of NAEK


title: 4c Hepatocytes [Hep_4c_126]


title: 4c Hepatocytes [Hep_4c_125]


title: AD, CBL sample 96--18

description:
Alzheimer's CBL sample
CBL 96--18

source_name: CBL sample 96--18


title: DKO ACE-I 3

value: captopril (10 mg/kg/day)


title: DKO ACE-I 2


title: AD, CBL sample 96--05

description:
Alzheimer's CBL sample
CBL 96--05

source_name: CBL sample 96--05


title: Transgenic cells +NAEK 01_RNA-seq

description: in the present of NAEK


title: 4c Hepatocytes [Hep_4c_124]

value: Wistar


title: Transgenic cells +NAEK 02_RNA-seq

description: in the present of NAEK


title: 4c Hepatocytes [Hep_4c_123]


title: HEK293T cells_Ribo-seq

description:
Ribosome protected mRNA
in the present of NAEK

data_processing:
Ribosome footprints were trimmed for 3'adaptor
Mapping to TAG terminated transcripts via Bowtie (maqerr: 70, seedlen: 25, maxbts: 125)
Genome_build: Homo sapiens genome (GRCh38.87)
Supplementary_files_format_and_content: xlsx files of ribosome footprint counts in the coding/extended regions of HEK293T cells

source_name: HEK293T cells

growth_protocol: HEK293T and transgenic cells were maintained in DMEM medium (Macgene) supplemented with 10% FBS (PAA) at 37 °C in a 5% CO2 incubator.

extract_protocol:
The ribosome footprint libraries of transgenic cells and HEK-293T cells were constructed using Illumina’s TrueSeq Ribo Profiling (Mammalian) Kit.
The ribosome footprint libraries of transgenic cells and HEK-293T cells were constructed using Illumina’s TrueSeq Ribo Profiling (Mammalian) Kit

treatment_protocol: In the present of NAEK.

tag: passages


title: 4c Hepatocytes [Hep_4c_122]


title: DKO 3


title: Transgenic cells_Ribo-seq


title: DKO ACE-I 1


title: DKO 2


title: AD, CBL sample 06--65

description:
Alzheimer's CBL sample
CBL 06--65

source_name: CBL sample 06--65

tag: plate


title: AD, CBL sample 07--09

description:
Alzheimer's CBL sample
CBL 07--09

source_name: CBL sample 07--09

tag: bead chip


title: 4c Hepatocytes [Hep_4c_120]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes


title: AD, CBL sample 06--54

description:
Alzheimer's CBL sample
CBL 06--54

source_name: CBL sample 06--54

tag: well position


title: 4c Hepatocytes [Hep_4c_121]


title: 4c Hepatocytes [Hep_4c_119]


title: AD, CBL sample 04--66

description:
Alzheimer's CBL sample
CBL 04--66

source_name: CBL sample 04--66

tag: tissue


title: AD, CBL sample 06--56

description:
Alzheimer's CBL sample
CBL 06--56

source_name: CBL sample 06--56

tag: gender


title: AD, CBL sample 99--10

description:
Alzheimer's CBL sample
CBL 99--10

source_name: CBL sample 99--10

tag: diagnosis


title: AD, CBL sample 01--11

description:
Alzheimer's CBL sample
CBL 01--11

source_name: CBL sample 01--11


title: WT ACE-I 3

source_name: Heart


title: WT ACE-I 1


title: 4c Hepatocytes [Hep_4c_117]


title: 4c Hepatocytes [Hep_4c_118]


title: 4c Hepatocytes [Hep_4c_116]


title: WT 3


title: 4c Hepatocytes [Hep_4c_115]


title: WT 2


title: AD, CBL sample 02--09

description:
Alzheimer's CBL sample
CBL 02--09

source_name: CBL sample 02--09


title: AD, CBL sample 01--15

description:
Alzheimer's CBL sample
CBL 01--15

source_name: CBL sample 01--15


title: 4c Hepatocytes [Hep_4c_113]


title: thiosulfate, biological rep1

city: Fuchu-shi

first: Ohtsu

last: Naoko

state: Tokyo

address: 3-5-8 Saiwai-cho

department: Biological Production

institute: Tokyo University of Agriculture and Technology

description: Gene expression data applied with thiosulfate as a thiosulfate

hyb_protocol: The cDNAs were hybridized with the Affymetrix Gene Chip Hybridization, Wash and Stain Kit (Thermo Fisher Scientific, Waltham, MA, USA) to the Affymetrix GeneChipTM Arabidopsis Gene 1.0 ST Array (Thermo Fisher Scientific, Waltham, MA, USA).

scan_protocol: The scanned fluorescent images were analyzed with Affimetrix GeneChip Command Console Software (Thermo Fisher Scientific, Waltham, MA, USA) to generate a CEL file and with the Affimetrix Expression Console (Thermo Fisher Scientific, Waltham, MA, USA) to generate a CHP file.

data_processing: The CHP file was analyzed with Transcriptome Analysis Console Software (v. 4.0, 64-bit) (Thermo Fisher Scientific, Waltham, MA, USA). The Robust Multiarray Average method (Irizarry et al. 2003) was used to normalize the microarray signal values.

organism: Arabidopsis thaliana

source_name: Arabidopsis roots hydroponically grownt for 8 weeks

label_protocol: The cRNA synthesis and the subsequent single-strand cDNA synthesis were performed with the Affymetrix GeneChip WT Plus Reagent Kit (Thermo Fisher Scientific, Waltham, MA, USA). The single-strand cDNAs was labeled with the Affymetrix GeneChip WT Terminal labeling kit (Thermo Fisher Scientific, Waltham, MA, USA).

growth_protocol: Arabidopsis Col-0 WT plants were hydroponically grown at 22C  for 8 wks under short day condition using MGRL medium (Fujiwara et al., 1992) in which all of sulfate ions were replaced with chloride ions.

extract_protocol: Total RNA was extracted from roots using the RNeasy mini kit (Qiagen, Hilden, Germany) combined with the RNase-Free DNase Set (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Sulfur source was applied as 300 μM of sodium sulfate or 150 μM of sodium thiosulfate.

value: roots

value: Col-0 WT

value: 8 weeks old

value: 150 μM of sodium thiosulfate


title: sulfate, biological rep2

description: Gene expression data applied with sulfate as a sulfur source

value: 300 μM of sodium sulfate


title: thiosulfate, biological rep2


title: AD, CBL sample 08--29

description:
Alzheimer's CBL sample
CBL 08--29

source_name: CBL sample 08--29

value: brain

value: CBL


title: AD, CBL sample 02--29

description:
Alzheimer's CBL sample
CBL 02--29

source_name: CBL sample 02--29

value: F

value: AD


title: WT 1

value: whole heart

value: post natal 24 weeks


title: thiosulfate, biological rep3


title: sulfate, biological rep1


title: sulfate, biological rep3


title: WT ACE-I 2


title: AD, CBL sample 07--27

description:
Alzheimer's CBL sample
CBL 07--27

source_name: CBL sample 07--27


title: Kcnh2_Prom_AdultLiver_4C

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

library_source: genomic

data_processing:
Library strategy: 4C-seq
4C templates were mixed and sequenced simultaneously in 1 Illumina HiSeq 2000 lane. The sequence tags generated by the procedure were prefixed by the 4C reading primer, which includes the DpnII restriction site sequence. The 4C reading primer sequences were separated from multiplexed 4C-seq libraries, and the suffixes were extracted for further processing.
Mapping and filtering of the sequence reads was done as previously described (Werken et al., 2012, Nat Methods). The algorithm constructs a background model for remote intra- and interchromosomal contacts to correct for systematic biases that can occur during the 4C-seq experimental protocol. The algorithm is designed to use controls for sequencing errors and nonunique sequences while considering the high coverage (100×–100,000×) of fragment ends that are proximal to the viewpoint fragment.
To normalize the interactions in close proximity to the viewpoint, the algorithm was used to calculate the median of normalized coverage for running windows of size 4 kb and sliding windows of 2–50 kb of linearly increasing size. All median values represent enrichment relative to the maximum attainable 4-kb median value, whereas sliding windows represent enrichment relative to the maximum attainable 12-kb median value. The 20th and 80th percentiles were also computed and depicted as the gray area around the 4-kb running windows.
The 4C-seq contact profile comparison plots were generated combining the mapping (Werken et al., 2012, Methods Enzymol) and normalization (Werken et al., 2012, Nat Methods) strategies. Within samples the distribution of the blind fragment-end reads and the distribution of the non-blind fragment-end reads were quantile normalized after linear interpolation of the center of the fragment-end using R's limma package (Smyth, 2005). The reads between samples were normalized based on library size within the locus. Subsequently, a running trimmed (10%) mean was calculated on 21 fragment-ends to smoothen the 4C-seq data. The R statistical package version 3.1.0 was used for the statistical calculations and for generating the 4C-Seq plots (R Core Team, 2013).
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle tracks contain uniquely mapped reads at 4C fragment ends on the cis chromosome, i.e. the chromosome on which the bait/viewpoint fragment is located (chr4). Scores represent the number of reads mapping to a DpnII restriction fragment end.

source_name: Adult Liver

growth_protocol: Animal care was in accordance with guidelines from the European Union and Amsterdam University Medical Centers. Tbx3Venus mice were maintained on a FVB/NJ background commercially obtained from Jackson laboratory (stock number 100800).

extract_protocol:
Adult mouse hearts and livers were isolated in ice cold PBS. Single cell suspensions were obtained by dissociation of tissue with IKA Ultra Turrax T5 FU, followed by dounce homogenization. Chromatin was cross-linked with 2% formaldehyde in PBS with 10% FCS for 10 min at room temperature, nuclei were isolated and cross-linked DNA was digested with a primary restriction enzyme recognizing a 4 bp restriction site (DpnII), followed by proximity ligation. Cross-links were removed and a secondary restriction enzyme digestion (Csp6I), followed again by proximity ligation.
200 ng of the resulting 4C template was used for subsequent PCR reactions using Expand Long Template Polymerase (Roche). PCR products were purified using the High Pure PCR Product Purification Kit (Roche, 11732676001).

treatment_protocol: No treatment conducted

value: FVB/NJ

value: adult:2-4 months

value: whole liver


title: 4c Hepatocytes [Hep_4c_114]

value: Female


title: Kcnh2_CRE11_AdultLiver_4C


title: Kcnh2_CRE11_AdultHeart_4C

source_name: Adult Heart


title: AD, CBL sample 07--15

description:
Alzheimer's CBL sample
CBL 07--15

source_name: CBL sample 07--15

value: M


title: Kcnh2_Prom_AdultHeart_4C


title: 4c Hepatocytes [Hep_4c_112]

value: Wistar


title: AD, CBL sample 08--07

description:
Alzheimer's CBL sample
CBL 08--07

source_name: CBL sample 08--07


title: 4c Hepatocytes [Hep_4c_110]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes


title: SCLE skin lesion_H6_020_144_SCLE

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description: Gene expression data from human sCLE skin lesion

hyb_protocol: Biotin labeled cDNA was fragmented and hybridized to Affymetrix Human Gene 2.1  ST arrays (Santa Clara, CA) according to the manufacturer protocol.

scan_protocol: GeneChip arrays were scanned by using the Affymetrix GeneTitan system (software version 3.2.4.1515) according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using R software version 3.1.3 using custom CDF version 19 and modified Affymetrix_1.44.1 package from BrainArray: RMA method and Human Entrez Gene custom CDF annotation version 19 were used for the normalization; and Combat for batch correction.

source_name: SCLE skin lesion

label_protocol: Biotinylated cRNA were prepared using the NuGEN Encore Biotin Module (Encore Biotin Module Manual, P/N M01111 v6) following the manufacturer's protocol.

extract_protocol: Total RNA was isolated using the E.N.Z.A. FFPE RNA Kit (Omega Bio-tek) following manufacturer’s instructions.

tag: disease state

value: SCLE

value: Skin biopsy


title: SCLE skin lesion_H6_023_147_SCLE


title: SCLE skin lesion_H6_011_132_SCLE


title: 4c Hepatocytes [Hep_4c_108]


title: SCLE skin lesion_H6_021_145_SCLE


title: G1297 Dox OFF H3K27ac input

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

data_processing:
The sequencing quality was checked using fastqc.
Low quality sequencing reads were trimmed and sequencing adaptor sequences were removed using cutadapt (-e 0.05 -O 4 -q 20 -m 31).
The trimmed reads were mapped to mm10 using bowtie2 (--very-sensitive).
Reads which had low mapq (<30), mapped to blacklisted regions or were duplicates were removed using samtools and picard.
bigWig files were generated using deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: G1297 cell line

growth_protocol: G1297; DMEM + 10% FBS, PS/ MEFs; DMEM + 10%FBS, PS, NEAA, L-Glu, 2-ME/ iPSCs;  Knockout DMEM + 15%FBS, PS, NEAA, L-Glu, 2-ME, LIF

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies; anti-HA mouse monoclonal antibody, Nacalai cat# 06340-54; anti-H3K27ac mouse monoclonal antibody, Wako MABI0309.
Libraries were prepared according to the manual of Illumina's Trueseq ChIP sample prep kit set A (Part# IP-202-1012).

treatment_protocol: "Dox ON" samples were treated with Doxycycline (0.2µg/ml) containing medium for indicated time.

tag: cell line

tag: antibody


title: AD, CBL sample 03--04

description:
Alzheimer's CBL sample
CBL 03--04

source_name: CBL sample 03--04

tag: brain region


title: G1297 Dox OFF H3K27ac rep#1

value: anti-H3K27ac mouse monoclonal antibody, Wako MABI0309


title: 4c Hepatocytes [Hep_4c_107]


title: AD, CBL sample 05--35

description:
Alzheimer's CBL sample
CBL 05--35

source_name: CBL sample 05--35


title: 4c Hepatocytes [Hep_4c_111]


title: 4c Hepatocytes [Hep_4c_109]


title: SCLE skin lesion_H6_018_142_SCLE


title: G1297 Dox ON H3K27ac rep#2

value: Doxycycline (0.2µg/ml)


title: G1297 Dox ON H3K27ac rep#1


title: G1297 Dox OFF H3K27ac rep#2


title: AD, CBL sample 04--16

description:
Alzheimer's CBL sample
CBL 04--16

source_name: CBL sample 04--16


title: 4c Hepatocytes [Hep_4c_105]


title: AD, CBL sample 98--10

description:
Alzheimer's CBL sample
CBL 98--10

source_name: CBL sample 98--10


title: 4c Hepatocytes [Hep_4c_106]


title: SCLE skin lesion_H6_010_131_SCLE


title: G1297 Dox ON H3K27ac input


title: AD, CBL sample 02--39

description:
Alzheimer's CBL sample
CBL 02--39

source_name: CBL sample 02--39


title: 4c Hepatocytes [Hep_4c_104]


title: 4c Hepatocytes [Hep_4c_103]


title: Sarcoma-MEF Dox ON HA 12h rep#2

source_name: MEF

value: MEF

value: anti-HA mouse monoclonal antibody, Nacalai cat# 06340-54


title: DKO 1

source_name: Heart

tag: genotype

value: LDLR-/- and ob/ob


title: Sarcoma-MEF Dox ON HA 12h rep#1


title: AD, CBL sample 97--08

description:
Alzheimer's CBL sample
CBL 97--08

source_name: CBL sample 97--08

value: brain

value: CBL


title: AD, CBL sample 96--46

description:
Alzheimer's CBL sample
CBL 96--46

source_name: CBL sample 96--46

value: AD


title: 4c Hepatocytes [Hep_4c_102]


title: Sarcoma-MEF Dox ON HA input


title: G1297 Dox ON 12h HA rep#2


title: AD, CBL sample 97--25

description:
Alzheimer's CBL sample
CBL 97--25

source_name: CBL sample 97--25

value: F


title: AD, CBL sample 05--57

description:
Alzheimer's CBL sample
CBL 05--57

source_name: CBL sample 05--57


title: 4c Hepatocytes [Hep_4c_100]


title: 4c Hepatocytes [Hep_4c_101]


title: AD, CBL sample 96--50

description:
Alzheimer's CBL sample
CBL 96--50

source_name: CBL sample 96--50


title: G1297 Dox ON HA input


title: G1297 Dox ON 12h HA rep#1


title: ch12_wt_mRNA_APR0h

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description:
mRNA-Seq
mRNA
ercc-spike-in

data_processing:
Base calling: Illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
ATAC-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ATAC-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ATAC-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragment and low quality reads (MAPQ <30)
HiC-Seq: generate contact matrix: juicer running with default parameter
4C-Seq: filtering: each read pair was tested for the presence of a perfect match to the respective bait primer as well as the bait spacer between the end of the primer and the restriction sites used in the corresponding experiment.
4C-Seq: mapping: bowtie-1.1.1/bowtie -X 500 -p 3 -v2 -k2 -m1 --phred64-quals -sam
4C-Seq: frequency: assign to NlaIII/CSP6i fragment (human) or DpnII/CSP6i fragment (mouse)to calculate fraction of restriction fragments for which 4C reads were found
CRISPR screen: Build artificial genome with primer and sgRNA constructs and make index with bowtie
CRISPR screen: alignment: bowtie -S -m 1 -p 4 -a --best --strata -n 2 -l 80
CRISPR screen: filtering and sort: samtools view -S -b -F4 | samtools sort -@ 2
CRISPR screen: samtools idxstats on aligned file
CRISPR screen: calculate frequency of each sgRNAs in each pool
CRISPR screen: samtools idxstats on aligned file
Genome_build: mm9 (MGSCv37), hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm).
Supplementary_files_format_and_content: ATAC-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm).
Supplementary_files_format_and_content: HiC-Seq: .hic format including contact matrix, normalization information generated by juicer.sh.
Supplementary_files_format_and_content: 4C-Seq: bed file showing read frequency in 100K window normalized by the number of fragments in each window.
Supplementary_files_format_and_content: mRNA-Seq:.wig files tag density divided by library size in millions to obtain normalized read density (rpkm).
Supplementary_files_format_and_content: CRISPRscreen: summarized text file on each codition, replicates, gene, sgRNAs.

source_name: CH12 B cell line

growth_protocol: Cas9 expressing cells: Primary CD4+ cells expressing Cas9 were isolated from a Cas9 expressing mouse (Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh) (Platt et al., Cell, 2014). Spleen was triturated in DMEM, supernatant was filtered and immediately processed according to the MACS mouse CD4+ T Cell Isolation Kit (Miltenyi Biotec, Cologne, Germany), following the manufacturer’s protocol. Isolated cells were seeded in a six-well plate that was previously coated with aCD3 and aCD28 at a final concentration of 10 ug/mL in 1.6 mL of PBS. The plate was incubated at 37°C for a minimum of 30 min. The PBS was then removed and the cells added to the plate. Cas9 expression in E14 ES cells was obtained through infection with lentiCas9-blast virus (Addgene plasmid #52962). After Blasticidin selection (7.5 ug/mL), clones expressing Cas9 were isolated and expanded to be used for the multiCRISPR screen for essential Mediator subunits. Cas9 expression was assessed by Western blot analysis and cutting efficiency after transfection with sgRNA plasmids.

extract_protocol:
Extraction protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with MNase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at 37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or MNase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. MNase-Seq: 4x10^7 resting and activated B cells were digested with 24 different concentrations of MNaseI. After an initial RT-qPCR analysis and curve-fitting, the MNaseI concentrations for the most representative nucleosomal fraction was determined. The lowest three nucleosomal fractions (which corresponded to MNaseI concentrations of 0U, 0U, and 0.0026U) were pooled together and used as input control. Nucleosomal fractions 16-18 (which corresponded to enzyme concentrations of 0.068U, 0.045U, and 0.03U) were also pooled for further processing. Input samples were sonicated to obtain similar fragment sizes as the MNaseI-digested samples. DNA was then concentrated and each sample was spiked with 0.055mg of l DNA (also sonicated to match the sample size as was input DNA).
HiC-Seq: We used the same protocol for in situ HiC libraries as Rao et al., (Cell, 2014 Dec; 159:1-16).
4C-seq: The 4C assay was performed as previously described van de Werken et al. (2012) with minor modifications. Ten million of CH12 B cell line were crosslinked in 2% formaldehyde at 37°C for 10 min. The reaction was quenched by the addition of glycine (final concentration of 0.125 M). Cells were then washed with cold PBS and lysed (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40, 1× complete protease inhibitors [Roche]) at 4°C for 1 hr. Nuclei were incubated at 65°C for 30 min, 37°C for 30 min in 500 μl of restriction buffer (New England BioLabs DpnII buffer) containing 0.3% SDS. To sequester SDS, Triton X-100 was then added to a final concentration of 1.8%. DNA digestion was performed with 400 U of DpnII (New England Biolabs) at 37°C overnight. After heat inactivation (65°C for 30 min), the reaction was diluted to a final volume of 7 ml with ligation buffer containing 100 U T4 DNA Ligase (Roche) and incubated at 16°C overnight. Samples were then treated with 500 μg Proteinase K (Ambion) and incubated overnight at 65°C to reverse formaldehyde crosslinking. DNA was then purified by phenol extraction and ethanol precipitation. For circularization, the ligation junctions were digested with Csp6I (Fermentas) at 37°C overnight. After enzyme inactivation and phenol extraction, the DNA was religated in a 7 ml volume (1,000 U T4 DNA Ligase, Roche). Three micrograms of 4C library DNA was amplified with Expand Long template PCR System (Roche). Thermal cycle conditions were DNA denaturing for 2 min at 94°C, followed by 30 cycles of 15 s at 94°C, 1 min at 58°C, 3 min at 68°C, and a final step of 7 min at 68°C. Bait was amplified with inverse PCR primers as follows: 3RR with DpnII: _4C 5′- GCTTATCTGTAAAGAATGGGTC-3′, 3RR_Csp6i 5′-GGCCTTAGAAGGCTCTGTAC-3′. 4C-amplified DNA was microsequenced with the Illumina platform.
mRNA-seq: Total RNA from 10^6 of WT or ZF9-11 CH12 cells was isolated by Trizol extraction. mRNA was then isolated. ERCC-spike-in was added on some samples for quantitative comparison between two conditions.
ATACseq: One hundred thousand cultured cells were harvested for each point. Cell lysis and Transposition reaction were immediately performed according to Greenleaf’s group protocol (Corces et al., Nat Meth 2017; Buenrostro et al., Nat Meth 2013). Transposed DNA was immediately purified and stored at -20C before library preparation according to the above protocol.
CRISPRscreen: Cells were harvested at an early reference time-point (second day after infection) and two late time-points (14 and 21 days after infection). DNA was extracted using DNeasy Blood and tissue kit according to the manufacturer’s instructions (#69506, Qiagen).
Library construction protocol:
ChIP-Seq  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 2500 or 3000 (Illumina).
HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 2500 (Illumina).
4C-seq: DNA was prepared for paired-end Illumina sequencing. 50 cycles of sequencing data were acquired on the HiSeq 2500 (Illumina).
mRNA-seq: Standard RNA-Seq library preparation was performed following Illumina's RNA-Seq protocol v2. 50 cycles of sequencing data were acquired on HiSeq 2000, 2500 or 3000 (Illumina).
ATAC-seq: DNA was prepared for single-end Illumina sequencing. 50 cycles of sequencing data were acquired on the HiSeq 2000 (Illumina).
CRISPRscreen: DNA was prepared for single-end Illumina sequencing using staggered GeCKO readout primers (Shalem et al. 2013). 80 cycles of sequencing data were acquired on the MiSeq (Illumina).

treatment_protocol: CRISPR infection: The viral libraries which contain sgRNAs were used to infect Cas9 expressing E14 ES cells and primary CD4+ T cells isolated from the Rosa26-Cas9 expressing mice. Two hundred thousand cells were seeded in a six-well plate the day before infection. Concentrated viruses were added to the media in presence of Polybrene (6 ug/mL). The amount of virus was adjusted according to the viral titer to obtain a MOI of 0.3. Cells were transduced by spinfection at 1,350g for 90 min and 28-32°C. Infected cells were selected 24h after infection, using Puromycin at a final concentration of 1 ug/ml for ES cells and 2 ug/mL for CD4+ T cells.

tag: cell type

value: lymphoma cell line

tag: genotype/variation

value: WT


title: 4c Hepatocytes [Hep_4c_99]

data_processing:
Expression levels were normalized with Actb.
A -deltaCt value normazized to Actb is used as a gene expression level for each gene.

tag: strain


title: SCLE skin lesion_H6_004_125_SCLE


title: AD, CBL sample 06--30

description:
Alzheimer's CBL sample
CBL 06--30

source_name: CBL sample 06--30

tag: age


title: 4c Hepatocytes [Hep_4c_97]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes

tag: Sex


title: SCLE skin lesion_H6_003_124_SCLE

source_name: SCLE skin lesion


title: 4c Hepatocytes [Hep_4c_96]


title: SCLE skin lesion_H6_006_127_SCLE


title: AD, CBL sample 05--01

description:
Alzheimer's CBL sample
CBL 05--01

source_name: CBL sample 05--01


title: SCLE skin lesion_H6_001_122_SCLE


title: SCLE skin lesion_H5_020_120_SCLE


title: SCLE skin lesion_H5_021_121_SCLE


title: 4c Hepatocytes [Hep_4c_98]


title: SCLE skin lesion_H5_019_119_SCLE


title: SCLE skin lesion_H5_012_112_SCLE


title: AD, CBL sample 99--15

description:
Alzheimer's CBL sample
CBL 99--15

source_name: CBL sample 99--15


title: SCLE skin lesion_H5_013_113_SCLE


title: 4c Hepatocytes [Hep_4c_95]


title: SCLE skin lesion_H5_003_103_SCLE


title: AD, CBL sample 98--17

description:
Alzheimer's CBL sample
CBL 98--17

source_name: CBL sample 98--17


title: ch12_wt_mRNA_APR60h

description:
mRNA-Seq
mRNA
ercc-spike-in

tag: treatment


title: SCLE skin lesion_H5_018_118_SCLE


title: AD, CBL sample 06--42

description:
Alzheimer's CBL sample
CBL 06--42

source_name: CBL sample 06--42

tag: plate


title: SCLE skin lesion_H5_002_102_SCLE


title: 4c Hepatocytes [Hep_4c_94]


title: DLE skin lesion_H6_024_148_DLE

description: Gene expression data from human DLE skin lesion

source_name: DLE skin lesion

value: DLE


title: AD, CBL sample 99--52

description:
Alzheimer's CBL sample
CBL 99--52

source_name: CBL sample 99--52

tag: bead chip


title: 4c Hepatocytes [Hep_4c_93]

value: Female


title: ch12_Med14Nsmash_mRNA_APR60h

description:
mRNA-Seq
mRNA
ercc-spike-in


title: SCLE skin lesion_H5_017_117_SCLE


title: 4c Hepatocytes [Hep_4c_92]


title: AD, CBL sample 99--24

description:
Alzheimer's CBL sample
CBL 99--24

source_name: CBL sample 99--24

tag: well position

value: M


title: 4c Hepatocytes [Hep_4c_91]

value: Wistar


title: ch12_Med13mm_mRNA_c1

description:
mRNA-Seq
mRNA


title: AD, CBL sample 00--08

description:
Alzheimer's CBL sample
CBL 00--08

source_name: CBL sample 00--08

tag: tissue


title: ch12_Med12Lmm_mRNA_c1

description:
mRNA-Seq
mRNA


title: DLE skin lesion_H6_022_146_DLE


title: ch12_Med12Lmm_mRNA_c2

description:
mRNA-Seq
mRNA


title: DLE skin lesion_H6_019_143_DLE


title: ch12_Med14Nsmash_mRNA_APR0h

description:
mRNA-Seq
mRNA
ercc-spike-in


title: 4c Hepatocytes [Hep_4c_90]


title: DLE skin lesion_H6_016_140_DLE


title: AD, CBL sample 00--10

description:
Alzheimer's CBL sample
CBL 00--10

source_name: CBL sample 00--10

tag: gender


title: DLE skin lesion_H6_012_133_DLE


title: 4c Hepatocytes [Hep_4c_89]


title: SCLE skin lesion_H5_001_101_SCLE

value: SCLE


title: ch12_Med13mm_mRNA_c3

description:
mRNA-Seq
mRNA


title: DLE skin lesion_H6_009_130_DLE

value: Skin biopsy


title: ch12_Med13mm_mRNA_c2

description:
mRNA-Seq
mRNA


title: chrom-RNA_UT_rep3

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: Chromatin-associated RNA

data_processing:
Library strategy: chromatin-associated-RNA-seq
Single-end reads were pseudo-aligned to the reference transcriptome using Kallisto v0.44.0 (PMID: 27043002; quant -b 100 -l 300 -s 100)
Genome_build: cDNA Ensembl Release 92
Supplementary_files_format_and_content: *.tsv, transcripts abundances inferred using Kallisto

source_name: Primary bone marrow-derived macrophages (BMDM)

growth_protocol: Bone marrow cells isolated from C57BL/6 mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol: chromatin-associated-RNA-seq libraries were prepared for HiSeq2000 sequencing following standard protocols.

value: BMDM cells (7th day of differentiation)

value: No treatment

tag: library type

value: Unstranded


title: chrom-RNA_UT_rep2

description: Chromatin-associated RNA


title: 4c Hepatocytes [Hep_4c_88]

extract_protocol: Adult hepatocytes were isolated from Wistar rats by two-step collagenase perfusion. NPCs were harvested from the undigested remnant tissue by further digestiong with collagenase-hyaluronidase.


title: AD, CBL sample 00--22

description:
Alzheimer's CBL sample
CBL 00--22

data_processing:
Data was analyzed in R (version 3.4.2) using minfi (1.23.4) and SVA (3.26.0). Poorly performing probes (detection p-value < 0.05) and sex chromosome probes were removed from the analysis. NOOB and functional normalization were performed using the minfi package according author guidelines. Confounding variables were detected using SVA and, alongside batch/plate effects, were accounted for using the ComBat algorithm.
Normalized Average betas included as supplementary files (processedSamples*.txt) on the Series record.
Methylated and unmethylated signal intensities included as supplementary files (signalIntensities*.txt) on the Series record.

source_name: CBL sample 00--22

tag: diagnosis


title: chrom-RNA_UT_rep1

description: Chromatin-associated RNA


title: 4c Hepatocytes [Hep_4c_87]


title: AD, CBL sample 00--13

description:
Alzheimer's CBL sample
CBL 00--13

source_name: CBL sample 00--13


title: 4c Hepatocytes [Hep_4c_86]


title: 4c Hepatocytes [Hep_4c_85]


title: DLE skin lesion_H6_017_141_DLE

tag: disease state


title: AD, CBL sample 07--42

description:
Alzheimer's CBL sample
CBL 07--42

source_name: CBL sample 07--42


title: AD, CBL sample 02--19

description:
Alzheimer's CBL sample
CBL 02--19

source_name: CBL sample 02--19


title: chrom-RNA_LPS-4h_rep2

description: Chromatin-associated RNA

value: LPS (10 ng/ml) for 4hrs


title: 4c Hepatocytes [Hep_4c_84]


title: AD, CBL sample 03--37

description:
Alzheimer's CBL sample
CBL 03--37

source_name: CBL sample 03--37


title: chrom-RNA_LPS-4h_rep1

description: Chromatin-associated RNA


title: chrom-RNA_LPS-30min_rep3

description: Chromatin-associated RNA

value: LPS (10 ng/ml) for 30'


title: 4c Hepatocytes [Hep_4c_83]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes


title: AD, CBL sample 99--64

description:
Alzheimer's CBL sample
CBL 99--64

source_name: CBL sample 99--64

value: brain


title: AD, CBL sample 94--28

description:
Alzheimer's CBL sample
CBL 94--28

source_name: CBL sample 94--28

value: CBL


title: DLE skin lesion_H6_008_129_DLE


title: 4c Hepatocytes [Hep_4c_82]


title: AD, CBL sample 08--37

description:
Alzheimer's CBL sample
CBL 08--37

source_name: CBL sample 08--37

value: AD


title: chrom-RNA_LPS-30min_rep2

description: Chromatin-associated RNA


title: 4c Hepatocytes [Hep_4c_81]


title: AD, CBL sample 97--26

description:
Alzheimer's CBL sample
CBL 97--26

source_name: CBL sample 97--26

value: F


title: AD, CBL sample 96--17

description:
Alzheimer's CBL sample
CBL 96--17

source_name: CBL sample 96--17


title: chrom-RNA_LPS-30min_rep1

description: Chromatin-associated RNA


title: chrom-RNA_LPS-4h_rep3

description: Chromatin-associated RNA


title: 4c Hepatocytes [Hep_4c_80]


title: AD, CBL sample 96--11

description:
Alzheimer's CBL sample
CBL 96--11

source_name: CBL sample 96--11


title: chrom-RNA_LPS-2h_rep3

description: Chromatin-associated RNA

value: LPS (10 ng/ml) for 2hrs


title: 4c Hepatocytes [Hep_4c_79]


title: chrom-RNA_LPS-2h_rep2

description: Chromatin-associated RNA


title: DLE skin lesion_H6_007_128_DLE

source_name: DLE skin lesion


title: DLE skin lesion_H6_005_126_DLE


title: 4c Hepatocytes [Hep_4c_78]


title: DLE skin lesion_H5_010_110_DLE


title: DLE skin lesion_H5_016_116_DLE


title: DLE skin lesion_H5_014_114_DLE


title: DLE skin lesion_H6_002_123_DLE


title: AD, CBL sample 98--14

description:
Alzheimer's CBL sample
CBL 98--14

source_name: CBL sample 98--14


title: chrom-RNA_LPS-2h_rep1

description: Chromatin-associated RNA


title: 4c Hepatocytes [Hep_4c_77]


title: chrom-RNA_LPS-1h_rep3

description: Chromatin-associated RNA

value: LPS (10 ng/ml) for 1hrs


title: DLE skin lesion_H5_008_108_DLE

value: DLE


title: DLE skin lesion_H5_015_115_DLE


title: AD, CBL sample 03--52

description:
Alzheimer's CBL sample
CBL 03--52

source_name: CBL sample 03--52


title: DLE skin lesion_H5_009_109_DLE


title: 4c Hepatocytes [Hep_4c_76]

value: Female


title: 4c Hepatocytes [Hep_4c_75]


title: AD, CBL sample 97--48

description:
Alzheimer's CBL sample
CBL 97--48

source_name: CBL sample 97--48


title: DLE skin lesion_H5_007_107_DLE


title: 4c Hepatocytes [Hep_4c_74]


title: AD, CBL sample 04--28

description:
Alzheimer's CBL sample
CBL 04--28

source_name: CBL sample 04--28


title: 4c Hepatocytes [Hep_4c_73]


title: AD, CBL sample 06--52

description:
Alzheimer's CBL sample
CBL 06--52

source_name: CBL sample 06--52


title: H3K4me3_UT_rep2

description: Chromatin IP against H3K4me3 on Mnase-digested chromatin

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID: 18798982) with the following parameters: --gsize=mm --nomodel --nolambda --bw=100 --shiftsize=75.
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of peaks (MACS)

source_name: Primary bone marrow-derived macrophages (BMDM)

extract_protocol: ChIP-seq libraries were prepared for HiSeq2000 sequencing following standard protocols.

tag: antibody

value: Chromatin IP against H3K4me3


title: AD, CBL sample 06--67

description:
Alzheimer's CBL sample
CBL 06--67

source_name: CBL sample 06--67

extract_protocol: Tissue was incubated in lysis buffer (100 mM Tris HCL pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl, 100 ug/mL Proteinase K) overnight at 55°C.  and disassembled using a pestle. Disassociated tissue was treated with 4 uL of Rnase A for 30 minutes at RT and then treated with ethanol overnight at -20°C. 1 ug of extracted DNA per sample was treated with bisulfite and used in the assay.

tag: brain region


title: DLE skin lesion_H5_006_106_DLE


title: AD, CBL sample 07--08

description:
Alzheimer's CBL sample
CBL 07--08

source_name: CBL sample 07--08


title: 4c Hepatocytes [Hep_4c_72]

value: Wistar


title: DLE skin lesion_H5_005_105_DLE


title: DLE skin lesion_H5_004_104_DLE


title: AD, CBL sample 03--40

description:
Alzheimer's CBL sample
CBL 03--40

source_name: CBL sample 03--40

value: M


title: H3K4me3_LPS-4h_rep2


title: Normal skin_H6_015_139_C6_N

description: Gene expression data from human normal skin biopsy

source_name: Normal skin

value: Normal

value: Skin biopsy


title: chrom-RNA_LPS-1h_rep1

description: Chromatin-associated RNA

value: BMDM cells (7th day of differentiation)


title: H3K4me3_LPS-30min_rep2


title: chrom-RNA_LPS-1h_rep2

description: Chromatin-associated RNA

value: Unstranded


title: 4c Hepatocytes [Hep_4c_69]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes

value: 6 week old


title: AD, CBL sample 98--28

description:
Alzheimer's CBL sample
CBL 98--28

source_name: CBL sample 98--28


title: AD, CBL sample 99--39

description:
Alzheimer's CBL sample
CBL 99--39

source_name: CBL sample 99--39


title: Normal skin_H6_013_137_C4_N


title: 4c Hepatocytes [Hep_4c_68]


title: AD, CBL sample 99--13

description:
Alzheimer's CBL sample
CBL 99--13

source_name: CBL sample 99--13


title: H3K4me3_LPS-4h_rep1

value: LPS (10 ng/ml) for 4hrs


title: 4c Hepatocytes [Hep_4c_71]


title: 4c Hepatocytes [Hep_4c_70]


title: H3K4me3_UT_rep1

value: No treatment


title: 4c Hepatocytes [Hep_4c_67]


title: AD, CBL sample 00--28

description:
Alzheimer's CBL sample
CBL 00--28

source_name: CBL sample 00--28

value: brain

value: CBL


title: RWY109-S

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

description: sorted S phase sample

data_processing:
Sequence reads were mapped using Bowtie2 (version 2.2.5).
Unique reads mapping to a single genomic location were summed in 1 kb bins, using Samtools (version 1.3.1) and Bedtools (version 2.26.0).
Genome_build: sacCer3
Supplementary_files_format_and_content: BED files containing number of unique reads in 1 kb bins

organism: Saccharomyces cerevisiae

source_name: RWY109 strain, sorted S phase population

growth_protocol: Cells were harvested from mid-log phase cultures grown in YPDA medium.

extract_protocol:
DNA was purified by phenol chloroform extraction.
Library preparation was carried out according to NEBUltra II instructions.

treatment_protocol: Cells were sorted by DNA content (Sytox Green), selecting for S phase single cells.

value: MATa/alpha; trp1/trp1; dbf4{delta}::TRP/dbf4{delta}::TRP; his3::PDBF4 dbf4-4A::HIS/his3::PDBF4 dbf4-4A::HIS; sld3-38A-10his-13myc::KanMX/sld3-38A-10his-13myc::KanMX; mcm4{delta}74-174/mcm4{delta}74-174; sml1{delta}::URA3/sml1{delta}::URA3

tag: strain background


title: H3K4me3_LPS-2h_rep1

tag: cell type

value: LPS (10 ng/ml) for 2hrs


title: H3K4me3_LPS-2h_rep2


title: AD, CBL sample 00--18

description:
Alzheimer's CBL sample
CBL 00--18

source_name: CBL sample 00--18

value: F

value: AD


title: 4c Hepatocytes [Hep_4c_65]

value: Female


title: AD, CBL sample 99--60

description:
Alzheimer's CBL sample
CBL 99--60

source_name: CBL sample 99--60


title: 5-8F/DDP cell culture 2

city: Guangzhou

first: Jian

last: Zhang

address: 78 Hengzhigang Road, Guangzhou

institute: Affiliated Cancer Hospital & Institute of Guangzhou Medical University

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) used for basecalling
We used the StringTie software (v1.2.3) to estimate the abundance of the gene level and transcript level, referring to the official
Sequenced reads was filtered through Solexa CHASTITY, and to match to the corresponding reference genome HG19, by Hisat2 software
Genome_build: HG19
Supplementary_files_format_and_content: Xlsx include FPKM values for all sample

source_name: nasopharyngeal carcinoma cell line 5-8F

growth_protocol: 5-8F and 5-8F DDP-chemoresistance cell line (5-8F/DDP),  were cultured in RPMI-1640 (Gibco, Life Technologies, Carlsbad, CA, USA) supplemented with 5% fetal bovine serum.

extract_protocol:
Cells were washed by PBS, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 5-8F-DDP was selected and established by increasing concentrations of DDP until 2.5 μg/ml for more than 6 months to establish the DDP-resistant cells.

tag: ddp chemoresistance

value: 2.5 microg/ml DDP in 5percent FBS

tag: cell line

tag: tag

value: 2.5 μg/ml DDP in 5% FBS


title: 4c Hepatocytes [Hep_4c_64]

first: Takeshi

last: Katsuda

address: 421 Curie Blvd, BRB II/III Rm531

institute: University of Pennsylvania

tag: strain

value: Wistar

tag: age

tag: Sex


title: AD, CBL sample 00--35

first: Danielle

last: Brokaw

address: Biodesign Institute Building C, 1001 S McAllister Ave

institute: Arizona State University

description:
Alzheimer's CBL sample
CBL 00--35

source_name: CBL sample 00--35

tag: plate

tag: bead chip

value: M


title: 5-8F/DDP cell culture 3


title: 4c Hepatocytes [Hep_4c_66]


title: H3K4me3_LPS-30min_rep1

tag: treatment

value: LPS (10 ng/ml) for 30'

value: Chromatin IP against H3K4me3


title: AD, CBL sample 00--56

description:
Alzheimer's CBL sample
CBL 00--56

source_name: CBL sample 00--56

tag: well position

tag: tissue

tag: gender


title: 5-8F cell culture 3

value: 5percent FBS

value: 5% FBS


title: AD, CBL sample 01--43

description:
Alzheimer's CBL sample
CBL 01--43

source_name: CBL sample 01--43

tag: diagnosis


title: 5-8F cell culture 2


title: 5-8F cell culture 1


title: RWY012-S

description: sorted S phase sample

source_name: RWY012 strain, sorted S phase population

tag: genotype/variation

value: ade2/ade2; ura3/ura3; his3/his3; trp1/trp1; leu2/leu2; sml1::URA3/sml1::URA; rad53::LEU2/rad53::LEU2; MATa/MATalpha


title: 4c Hepatocytes [Hep_4c_62]

value: 6 week old


title: H3K4me1_UT_rep1

description: Chromatin IP against H3K4me1 on Mnase-digested chromatin

source_name: Primary bone marrow-derived macrophages (BMDM)

value: BMDM cells (7th day of differentiation)

value: No treatment

tag: antibody

value: Chromatin IP against H3K4me1


title: H3K4me3_LPS-1h_rep2

value: LPS (10 ng/ml) for 1hrs


title: H3K4me1_UT_rep2


title: H3K4me1_LPS-4h_rep2

value: LPS (10 ng/ml) for 4hrs


title: H3K4me1_LPS-4h_rep1


title: 5-8F/DDP cell culture 1


title: H3K4me3_LPS-1h_rep1


title: H3K4me1_LPS-30min_rep2


title: 4c Hepatocytes [Hep_4c_60]


title: AD, CBL sample 07--17

description:
Alzheimer's CBL sample
CBL 07--17

source_name: CBL sample 07--17

value: brain

tag: brain region

value: CBL

value: AD


title: 4c Hepatocytes [Hep_4c_63]

value: Female


title: 4c Hepatocytes [Hep_4c_59]

value: Wistar


title: H3K4me1_LPS-30min_rep1

tag: cell type


title: AD, CBL sample 08--10

description:
Alzheimer's CBL sample
CBL 08--10

source_name: CBL sample 08--10

value: F


title: 4c Hepatocytes [Hep_4c_58]


title: AD, CBL sample 08--46

description:
Alzheimer's CBL sample
CBL 08--46

source_name: CBL sample 08--46


title: H3K4me1_LPS-2h_rep2

value: LPS (10 ng/ml) for 2hrs


title: H3K4me1_LPS-2h_rep1


title: Normal skin_H6_014_138_C5_N

source_name: Normal skin

tag: disease state

value: Normal

value: Skin biopsy


title: 4c Hepatocytes [Hep_4c_57]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes


title: AD, CBL sample 01--13

description:
Alzheimer's CBL sample
CBL 01--13

source_name: CBL sample 01--13


title: 4c Hepatocytes [Hep_4c_56]


title: AD, CBL sample 08--05

description:
Alzheimer's CBL sample
CBL 08--05

source_name: CBL sample 08--05


title: AD, CBL sample 08--20

description:
Alzheimer's CBL sample
CBL 08--20

source_name: CBL sample 08--20

value: M


title: AD, CBL sample 02--41

description:
Alzheimer's CBL sample
CBL 02--41

source_name: CBL sample 02--41


title: 4c Hepatocytes [Hep_4c_61]


title: H3K4me1_LPS-1h_rep1


title: ChIP-Seq_PC3_ ubH2A_rep2

first: Filippo

last: Giancotti

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT MD Anderson Cancer Center

data_processing:
Reads were trimmed by trimmomatic prior to alignment, as recommended by the ChIP kit manufacturer.
The trimmed reads were then aligned to the hg19 reference genome using bowtie2.
Only uniquely aligned reads were kept for downstream 45 analysis, with duplicate reads removed by the same tools software v1.9.
To visualize ChIP-seq signal at individual genomic regions, we generated bedGraph file by using HOMER software v4.10.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: Human prostatic adenocarcinoma

growth_protocol: PC3 cells were obtained from ATCC and cultured according to the manufacturers' instructions.

extract_protocol:
Cell nuclei from approximately 20 million formaldehyde crosslinked (1%; 10 minutes at room temperature) were isolated and chromatin was fragmented using sonicator (bioruptor). Lysate were cleared and protein-DNA complexes were isolated using target antibodies and protein-G coated magnetic beads. Chromatin IP was conducted following the standard protocol from ActiveMotif ChIP-IT High Sensitivity® (HS) Kit.
Libraries were prepared according to standard Illumina HiSeq 3000 protocol/Illumina HiSeq 4000. Samples were sequenced at Integrated Genomics Operation Core at UT MD Anderson Cancer Center.

tag: cell line

value: prostate; derived from metastatic site:bone

tag: disease

value: grade IV, adenocarcinoma

value: 62 years adult

tag: chip antibody

value: millipore, 05-678


title: AD, CBL sample 07--69

description:
Alzheimer's CBL sample
CBL 07--69

source_name: CBL sample 07--69

tag: age


title: H3K27ac_UT_rep2

description: Chromatin IP against H3K27ac on Mnase-digested chromatin

tag: strain

value: BMDM cells (7th day of differentiation)

value: No treatment

value: Chromatin IP against H3K27ac


title: Normal skin_H5_023_135_C2_N


title: Normal skin_H5_024_136_C3_N


title: AD, CBL sample 08--41

description:
Alzheimer's CBL sample
CBL 08--41

source_name: CBL sample 08--41

tag: plate

value: brain


title: ChIP-Seq_PC3_ubH2A_rep1


title: 4c Hepatocytes [Hep_4c_55]

value: 6 week old

tag: Sex


title: 4c Hepatocytes [Hep_4c_54]


title: AD, CBL sample 07--64

description:
Alzheimer's CBL sample
CBL 07--64

source_name: CBL sample 07--64

tag: bead chip

value: CBL

value: AD


title: 4c Hepatocytes [Hep_4c_53]

value: Wistar

value: Female


title: 4c Hepatocytes [Hep_4c_52]


title: Normal skin_H5_022_134_C1_N


title: H3K27ac_UT_rep1

tag: treatment


title: 4c Hepatocytes [Hep_4c_51]


title: AD, CBL sample 96--09

description:
Alzheimer's CBL sample
CBL 96--09

source_name: CBL sample 96--09

tag: well position

tag: tissue


title: H3K27ac_LPS-4h_rep2

value: LPS (10 ng/ml) for 4hrs


title: H3K27ac_LPS-4h_rep1


title: AD, CBL sample 97--21

description:
Alzheimer's CBL sample
CBL 97--21

source_name: CBL sample 97--21

tag: gender

tag: diagnosis


title: H5981_3_O_R

first: Thomas

last: Chan

address: Room623, Area 39, CUHK, Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
RNA-seq reads were aligned to the human reference genome (hg38) using Tophat2. After alignment, Cufflinks were employed to quantify and normalize the expression level (FPKM) of transcriptomes with the default setting.
BS-seq raw reads were trimmed by TrimGalore as single-end mode to remove adapter contamination and poor-quality reads. Trimmed reads were mapped to the hg38 human genome in single-end mode by Bismark. After filtering out the duplicate alignments, methylation calls were extracted by Bismark.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: BS-seq: tab-delimited text files including location, context and methylation information for each sample.

source_name: Oocyte

extract_protocol:
Follicle induction approach
Followed by the published protocol with several modifications, single-cell M&T-seq was performed on two human oocytes. Briefly, each denuded oocytes was transferred into a tube containing 2.5µl of RLT plus buffer (Qiagen) and 1µl of a 1:250,000 dilution of ERCC spike-in mixture A (Life Technologies). Then, a total of 10µl of streptavidin-coupled magnetic beads (Dynabeads, Life Technologies) conjugated to a modified oligo-dT primer (5’-biotin-triethyleneglycol-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT) was added into the cell lysate and they were incubated at room temperature for 20mins. After incubation, the tubes were placed on the magnet. The supernatant, containing gDNA, were transferred to a new tube, the wash buffer (50mM Tris-HCl, 75mM KCl, 3mM MgCl2, 10mM DTT, 0.5% Tween-20, 0.2x RNAse inhibitor) was applied to wash beads for four times and all the wash buffer were pooled with the original supernatant to minimize the loss of gDNA. After washing, RNA ligated to the beads were subjected to perform SMART-seq2 as the common protocol. While, gDNA in the supernatant were employed to construct scBS libraries using Pico Methyl-Seq Library Prep Kit (Zymo) followed the manual provided by the manufacturer. The yield of all sequencing libraries was measured by Qubit 2.0 Fluorometer (Thermo) and their quality was assessed by Agilent 2100 Bioanalyzer in DNA high sensitivity assay chips. Qualified libraries were sequenced on HiSeq 2500 platform (Illumina) generating 150bp paired-end reads.

value: Oocyte

value: female


title: 4c Hepatocytes [Hep_4c_50]


title: H5981_2_O_D


title: H3K27ac_LPS-30min_rep2

source_name: Primary bone marrow-derived macrophages (BMDM)

value: LPS (10 ng/ml) for 30'

tag: antibody


title: H5981_3_O_D


title: AD, CBL sample 02--35

description:
Alzheimer's CBL sample
CBL 02--35

source_name: CBL sample 02--35

tag: brain region

value: F


title: U2OS+As_UNR_Rep3

city: Coventry

first: Nigel

middle: Paul

last: Dyer

address: Gibbet Hill Road

institute: University of Warwick

data_processing:
Sequence data were aligned to Ensemble release GRCh38 of the human genome using Tophat release 2.1.1. incorporating Bowtie 2.2.5.
Read counts against individual genes were obtained using HTSeq against the Ensemble reference annotation GRCh38.84.gtf
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file gives read counts for each gene for each sample

growth_protocol: HeLa, U2OS and SaOS-2 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% foetal calf serum (FCS) (Biosera) at 37 °C in a humidified environment containing 5% carbon dioxide.

extract_protocol:
Cells were washed four times in PBS and then suspended in polysome lysis buffer (0.5% v/v NP40, 100 mM KCl, 5 mM MgCl2, 10 mM HEPES pH7.0) then incubated on ice for 5 min before being transferred to -80 °C for a period of no less than 8 h
Finally, the raw lysates were thawed on ice, centrifuged at 15000 x g at 4 °C for 15 min, then the supernatants collected and the pelleted debris discarded. The lysate was further purified by a second centrifugation at 15000 x g at 4 °C to separate the aqueous lysate from unwanted lipids.
To precipitate UNR and associated molecules, Protein A-conjugated Dynabeads (Life Technologies) were firstly incubated with either an antibody against UNR (polyclonal rabbit antibody, Novus Biologicals NBP1-71914) or a control IgG (Invitrogen 10500C) in PBS containing 0.01% (v/v) Tween-20 (PBST) in tubes attached to a rotating mixer for 1 h at room temperature.
Following this, the beads were similarly blocked at 4 °C in 0.1% (w/v) bovine serum albumin (BSA) in PBS. The beads were then washed twice in ice-cold PBST and then once in ice-cold NT2 buffer (50 mM Tris-HCl, pH 7.4; 150 mM NaCl; 1mM MgCl2; 0.05% [v/v] NP-40) before resuspension in NT2 containing 0.5 % (v/v) RNase OUT, 400 μM VRC and 1 mM DTT. Cleared lysate  was then added at 1 part to 9 parts bead suspension and mixed by rotation for 4 h at 4 °C.
The beads were then washed five times in ice cold NT2 and each sample divided, 4 parts for RNA analysis
RNA was extracted from immune complex-loaded beads using Trizol (Life Technologies) according to the manufacturer’s instructions. RNA-Seq cDNA libraries were then made using the low sample protocol from the Illumina TruSeq RNA sample preparation v2 guide, except that the oligo-dT selection step was omitted, where possible 100 ng of RNA was used per sample, and libraries were quantified using Qubit Fluorometry.  The libraries were normalised to 10 nM.

treatment_protocol: Oxidative stress was applied by adding growth medium containing 0.5 mM sodium arsenite (S7400, Sigma); control untreated cells were similarly re-fed with fresh medium alone.

value: Osteosarcoma

tag: stress

value: oxidative stress (0.5mM sodium arsenite)

tag: rip antibody (pulldown)

tag: replicate


title: 4c Hepatocytes [Hep_4c_49]

city: Philadelphia


title: 4c Hepatocytes [Hep_4c_48]


title: AD, CBL sample 04--44

city: Tempe

description:
Alzheimer's CBL sample
CBL 04--44

source_name: CBL sample 04--44

value: M


title: AD, CBL sample 96--20

description:
Alzheimer's CBL sample
CBL 96--20

source_name: CBL sample 96--20


title: 4c Hepatocytes [Hep_4c_47]


title: H3K27ac_LPS-30min_rep1

tag: cell type

value: BMDM cells (7th day of differentiation)


title: 4c Hepatocytes [Hep_4c_46]


title: AD, CBL sample 06--11

description:
Alzheimer's CBL sample
CBL 06--11

source_name: CBL sample 06--11


title: AD, CBL sample 04--29

description:
Alzheimer's CBL sample
CBL 04--29

source_name: CBL sample 04--29


title: AD, CBL sample 06--37

description:
Alzheimer's CBL sample
CBL 06--37

source_name: CBL sample 06--37


title: U2OS+As_UNR_Rep2

tag: cell line

tag: disease state

value: UNR (polyclonal rabbit antibody, Novus Biologicals NBP1-71914)


title: U2OS+As_UNR_Rep1


title: U2OS+As_IgG_Rep3

value: control IgG (Invitrogen 10500C)


title: H3K27ac_LPS-2h_rep1

tag: strain

value: LPS (10 ng/ml) for 2hrs

value: Chromatin IP against H3K27ac


title: H5981_2_O_R

tag: age


title: H3K27ac_LPS-1h_rep1

value: LPS (10 ng/ml) for 1hrs


title: 4c Hepatocytes [Hep_4c_45]

source_name: Percoll-treated and FACS-sorted 4c hepatocytes

value: 6 week old

tag: Sex


title: U2OS+As_IgG_Rep2


title: 4c Hepatocytes [Hep_4c_44]

value: Wistar


title: AD, CBL sample 99--43

description:
Alzheimer's CBL sample
CBL 99--43

source_name: CBL sample 99--43

tag: plate

tag: bead chip

value: brain

value: CBL

value: AD


title: C7C5F398: DN3_NMe_GSM-2

city: New York

first: Stuart

middle: Aidan

last: Quinn

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

description: ATACseq

data_processing:
Adapter sequences were trimmed from raw reads using cutadapt v1.16 and aligned to mm10 (GRCm38) using bowtie2 v2.3.3.1 in paired end mode.
Duplicate fragments were removed using samtools v1.7.
Accessible chromatin peaks were called using MACS2 v2.1.1 in BAMPE mode and pileup tracks generated using the SPMR normalization method.
Genome_build: GRCm38
Supplementary_files_format_and_content: bed (.broadPeak) files contain accessible chromatin peaks
Supplementary_files_format_and_content: bedGraph files contain pileup generated by MACS2 v2.1.1 using SPMR normalization

source_name: DN3 Thymocytes

extract_protocol: Library was generated using the protocol described in Buenrostro et al. (Nat Methods, 2013 - PMID: 24097267)

tag: genotype

value: NMe GATA site 1 and 2 homozygous mutant

value: DN3 thymocytes


title: AD, CBL sample 99--28

description:
Alzheimer's CBL sample
CBL 99--28

source_name: CBL sample 99--28

tag: well position

tag: tissue


title: 4c Hepatocytes [Hep_4c_43]

value: Female


title: C7C5F395: DN3_NMe_GSM-1

description: ATACseq


title: H3K27ac_LPS-2h_rep2

tag: treatment


title: U2OS-As_UNR_Rep3

value: Osteosarcoma

value: Control


title: U2OS+As_IgG_Rep1

value: oxidative stress (0.5mM sodium arsenite)


title: AD, CBL sample 01--02

description:
Alzheimer's CBL sample
CBL 01--02

source_name: CBL sample 01--02

tag: gender

value: F

tag: diagnosis


title: AD, CBL sample 01--07

description:
Alzheimer's CBL sample
CBL 01--07

source_name: CBL sample 01--07

tag: brain region


title: 4c Hepatocytes [Hep_4c_42]


title: C7C5F392: DN3_NMe_WT-2

description: ATACseq

value: NMe wild type


title: 4c Hepatocytes [Hep_4c_41]


title: C7C5F389: DN3_NMe_WT-1

description: ATACseq


title: U2OS-As_UNR_Rep2

tag: stress

tag: rip antibody (pulldown)

value: UNR (polyclonal rabbit antibody, Novus Biologicals NBP1-71914)


title: U2OS-As_UNR_Rep1

tag: replicate


title: AD, CBL sample 00--54

description:
Alzheimer's CBL sample
CBL 00--54

source_name: CBL sample 00--54

value: M


title: 4c Hepatocytes [Hep_4c_40]


title: s7C5F398: DN3_NMe_GSM-3

data_processing:
Raw reads were aligned to the mouse genome (mm10/GRCm38) using STAR (v2.5.3)  with 2-pass mapping and guided by the Gencode mouse genome annotation (vM16).
Raw counts were computed at the gene-level using featureCounts in R (Rsubread v1.28.1).
Counts were normalized to library size and differential gene expression analysis was performed using DESeq2 (v1.20.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2 normalized gene-level counts

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Micro Kit (cat number 74004).
GENEWIZ (South Plainfield, NJ) performed the RNA library preparations and next generation sequencing. The SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA) as per manufacturer’s protocol. Illumina Nextera XT library was used for library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. Final libraries were analyzed on the Agilent TapeStation for library sizing, and quantified using the Qubit dsDNA HS Assay Kit and by quantitative PCR using KAPA Library Quantification Kit. Sequencing was performed on an Illumina HiSeq platform using a 2x150 Paired End (PE) configuration to generate a data output of approximately 58 million reads per sample.

value: DN3 Thymocytes


title: AD, CBL sample 03--21

description:
Alzheimer's CBL sample
CBL 03--21

source_name: CBL sample 03--21


title: U2OS-As_IgG_Rep3

tag: cell line

value: control IgG (Invitrogen 10500C)


title: 4c Hepatocytes [Hep_4c_39]

value: 6 week old


title: s7C5F396: DN3_NMe_GSM-2


title: U2OS-As_IgG_Rep2

tag: disease state


title: s7C5F395: DN3_NMe_GSM-1

tag: strain


title: U2OS-As_IgG_Rep1


title: AD, CBL sample 01--18

description:
Alzheimer's CBL sample
CBL 01--18

source_name: CBL sample 01--18

tag: age


title: AD, CBL sample 03--06

description:
Alzheimer's CBL sample
CBL 03--06

source_name: CBL sample 03--06


title: 4c Hepatocytes [Hep_4c_37]

value: Wistar

tag: Sex


title: 4c Hepatocytes [Hep_4c_38]


title: s7C5F397: DN3_NMe_WT-3


title: s7C5F392: DN3_NMe_WT-2


title: SaOS+As_UNR_Rep3


title: 4c Hepatocytes [Hep_4c_36]


title: AD, CBL sample 01--16

description:
Alzheimer's CBL sample
CBL 01--16

source_name: CBL sample 01--16

tag: plate

value: brain


title: 4c Hepatocytes [Hep_4c_35]


title: s7C5F389: DN3_NMe_WT-1


title: SaOS+As_UNR_Rep2


title: SaOS+As_UNR_Rep1


title: AD, CBL sample 01--34

description:
Alzheimer's CBL sample
CBL 01--34

source_name: CBL sample 01--34

tag: bead chip

value: CBL


title: 4c Hepatocytes [Hep_4c_34]


title: 4c Hepatocytes [Hep_4c_33]


title: AD, CBL sample 08--30

description:
Alzheimer's CBL sample
CBL 08--30

source_name: CBL sample 08--30

value: AD


title: 4c Hepatocytes [Hep_4c_32]