title: unmodified RNA oligo designed from human 18S rRNA - RT-KTq I614Y - 2µMdATP

city: Konstanz

first: Luisa

middle: Barbara

last: Huber

state: Baden-Württemberg

address: Universitätsstraße 10

department: Department of Chemistry

institute: Universität Konstanz

data_processing:
Sequencing data were processed by using the open source software KNIME 4.6.2
Quality and sequence are read from the FastQ files
Read1 and Read 2 were merged giving the expected size of transcript (RNA oligo samples 109 bp & tRNA samples 69 bp)
High quality data were filtered and aligned to the RNA reference of the oligonucleotide or tRNA sequences (http://gtrnadb.ucsc.edu).
Reads were sorted into unique molecular identifier (UMI) families and family read numbers were counted.
Error calculation are performed in each UMI family having more than 10 or 15 (tRNA data) reads.
If 90 % of the reads within each family carry the misincorporation, the error is set to 1 (otherwise 0).
Afterwards, the error is calculated over all UMI families at each position of the transcript and plotted using Microsoft excel software
Supplementary files format and content: excel-files include position, reference RNA sequence and error rates
Library strategy: DNA Amplicon-Seq

organism: synthetic construct

source_name: human 18S rRNA, chemically synthesized oligo

growth_protocol: The S. cerevisiae strains were grown in standard YPD medium (20 g/L peptone, 20 g/L dextrose, 10 g/L yeast extract) at 30°C to exponential phase (0.6-0.7 OD600)

extract_protocol:
Total RNA from yeast cells was isolated using hot acid phenol. RNA concentration was measured on Nanodrop One and RNA quality was assessed by capillary electrophoresis using a PicoRNA Chip on Bioanalyzer 2100 (Agilent technologies). Yeast total tRNA fraction was enriched using NucleoBond RNA 80 kit (Macherey-Nagel). Briefly, 50-80 micrograms of total RNA were loaded onto AXR80 column previously equilibrated with RO buffer. The column was washed 4 times with R1 buffer and tRNA fraction was eluted using R2 buffer. The eluate was then precipitated with an equal volume of isopropanol and centrifuged. The pellet was washed with 80% ethanol, and dissolved with RNAse free water
For RNA oligo samples: RT-Reaction mix contained 225 nM RNA template (unmodified or modified oligonucleotide), 150 nM DNA reverse primer with overhang, 100 µM of each nucleotide and 2 nM RT-KTq variant in 1x RT-KTq reaction buffer (50 mM Tris-HCl (pH 9.2), 16 mM (NH4)2SO4, 25 mM MgCl2, 0.1% (v/v) Tween 20). After annealing of template/primer and heating the mixture to 55°C, 4 µL DNA polymerase in 1x RT-KTq reaction buffer was added to start reverse transcription (10 µL reaction volume). After 10 min reaction time, mixture was heated to 95°C for 5 min and annealing was allowed once again by cooling stepwise to 4°C. The reaction was heated to 55°C and 10 µL Superscript IV reaction mix (Invitrogen) was added to reach a final volume of 20 µL. Reactions contained finally 10 U/µL Superscript IV (Invitrogen), 300 µM dNTP each, 5 mM DTT and 1x Superscript IV RT buffer (Invitrogen). After primer elongation for 10 min at 55°C, the reaction was put on ice. For each DNA library, the described reverse transcription was performed three times and combined after reaction. 60 µL combined reaction mix was mixed with 240 µL Buffer NTC (Macherey-Nagel) and clean-up was conducted with NucleoSpin Gel and PCR clean-up kit (Macherey-Nagel) according to the manufacturer's specifications. Elution was achieved by adding 15 µL Milli-Q water and centrifugation for 1 min at 13.000 rpm. Then, RNA template was digested by addition of 0.05 U/µL RNase H (NEB) in 1x RNase H reaction buffer at 37°C for 20 min. Enzyme was inactivated by heat at 65°C for 20 min. Purification of DNA was performed by agarose gel electrophoresis (2.5 % agarose gel in 1x TAE buffer), excision of the respective bands and applying the NucleoSpin Gel and PCR clean-up kit (Macherey-Nagel). To achieve DNA binding to the columns, buffer NTC was added to the gel pieces (400 µL buffer per 100 mg gel) and incubated at 50°C until gel was dissolved. Elution was conducted in the same way as described above. Afterwards, DNA was repaired by using 0.1 µL PreCR Repair mix (NEB) with 100 µM of each dNTP, 1x NAD+ (provided by the manufacturer) and 1x ThermoPol reaction buffer (NEB) to reach 20 µL reaction volume. DNA repair was performed at 37°C for 20 min. Without any purification step, DNA was used as template for primer extension reaction with 0.02 U/µL Q5 Hot Start High-Fidelity DNA Polymerase (NEB), 200 µM of each dNTP, 300 nM DNA forward primer with overhang and 0.2x Q5 reaction buffer in 25 µL reaction volume. A one step cycling protocol was chosen where denaturation at 98°C for 1 min, annealing at 62°C for 45 s and finale extension at 72°C for 2 min were conducted. Reaction was analyzed and purified by agarose gel electrophoresis as described above. This time NTI buffer (Machery Nagel) was used for dissolving the gel pieces at 55°C. A second DNA repair with the PreCR mix (NEB) was conducted in the similar way as described above. UMI introduction was obtained by applying Q5 Hot Start High-Fidelity DNA Polymerase (NEB) in a three step PCR reaction. The reaction mixture contained 20 µL repair mix, 0.02 U/µL DNA polymerase, 200 nM forward and reverse primer and finally 0.2x Q5 reaction buffer to reach 25 µL reaction volume. After initial denaturation at 98°C for 2 min, two cycles with 98°C for 10 s, 62°C for 30 s and 72°C for 30 s were carried out followed by a final elongation step at 72°C for 2 min. Reaction was analyzed and purified by agarose gel electrophoresis as described above. Here, buffer NTI was diluted with Milli-Q in a ratio of 2:1 and afterwards used for dissolving gel pieces at 50°C. Concentration of the DNA was determined with a qPCR approach, where an oligonucleotide with the same length was applied as reference in different template concentrations. 1x NEBNext Ultra II Q5 Master Mix (NEB) was used for PCR with 400 nM fwd and rev primer, 1x sybr green I in 5 µL reaction volume. After a final denaturation step at 98°C for 1 min, a three step cycling protocol with 35 PCR cycles followed with 98°C 10 s, 60°C 30 s and 72°C for 30 s and finally an elongation step with 72°C for 2 min was conducted. Fluorescent intensity was measured at the end of each cycle and melting curves were determined at the end of the reaction. For analysis, Cq values of reactions with reference DNA were blotted against the decadic logarithm of the template concentrations and linear regression was created. DNA concentrations were calculated by using the linear predictor function. Results were multiplied by two since reference DNA was applied double stranded and target DNA in the analyzed samples was only present in the single stranded format. DNA was repaired once again by using 0.05 µL PreCR mix (NEB), 1x NAD+, 100 µM of each dNTP, 59.044 fM DNA and 1x ThermoPol reaction buffer (NEB) to reach 11.25 µL end volume. After reaction for 20 min at 37°C, DNA mix was directly used for Amplicon PCR. Here, 400 nM forward and reverse primer (equipped with Illumina Adapter Sequence and Indices), the entire repair mix (final DNA concentration 26.57 fM) and 1x NEBNext Ultra II Q5 Master Mix (NEB) was used for reaction in 25 µL end volume. After a final denaturation step at 98 °C for 5 min, a three step cycling protocol with 35 PCR cycles followed with 98°C 10 s, 70°C 30 s and 72°C for 30 s and finally an elongation step with 72°C for 2 min was conducted. Reaction was analyzed and purified by agarose gel electrophoresis as described above. To dissolve gel pieces, buffer NTI (Macherey Nagel) was diluted with Milli-Q water in ration 2:1 and 450 µL NTI mix was added to the gel pieces. After complete dissolving at 50°C, mixture was dilute once again with Milli‑Q water to reach a final volume of 1750 µL. DNA was loaded on the column and eluted with 20 µL Milli-Q water. After performing the repair reaction on the whole eluate as described above, DNA was purified by using the QIAEX II System (Qiagen). 2 µL particle slurry was used for each sample and elution of DNA was achieved by adding 18 µL Milli-Q to the dried beads, incubation for 5 min and taking 16 µL after centrifugation. The concentration of the final DNA library was determined by Quantus™ Fluorometer (Promega) and usually ranged between 20 and 85 nM. After quality control with Bioanalyzer 2100 (Agilent), DNA libraries were pooled and sequenced in paired-end mode (2*75 bp) on an IIlumina NextSeq2000 instrument. For tRNA samples: 300 ng RNA (isolated from S. cerevisiae) was annealed to 300 nM reverse primer (containing UMI sequence) in the similar way as described in the chapter above. Hybridized template/primer was added to the reaction mix containing 100 µM of d(G/C/T)TP (each) and 2 µM dATP in 1x RT-KTq reaction buffer (50 mM Tris-HCl (pH 9.2), 16 mM (NH4)2SO4, 25 mM MgCl2, 0.1% (v/v) Tween 20). After heating to 55°C, RT was started by adding 100 nM RT-KTq I614Y in 1x RT-KTq reaction buffer to reach a final reaction volume of 10 µL. After 1 h reaction time, mixture was heated to 95°C for 5 min and annealing was allowed once again by cooling to 4°C stepwise. The reaction was heated to 55°C and 10 µL Superscript IV reaction mix was added to reach a final volume of 20 µL. Reactions contained finally 10 U/µL Superscript IV (Invitrogen), 300 µM dNTP each, 5 mM DTT and 1x Superscript IV RT buffer (Invitrogen). After primer elongation for 10 min at 55°C, the reaction was put on ice. Reaction mix was mixed with 160 µL Buffer NTC (Macherey-Nagel) and clean-up was conducted with NucleoSpin Gel and PCR clean‑up XS kit (Macherey-Nagel) according to the manufacturer's specifications. Elution was achieved by adding 16 µL elution buffer (Machery-Nagel). DNA was used for second UMI Introduction with 0.02 U/µL Q5 Hot Start High-Fidelity DNA Polymerase (NEB), 200 µM of each dNTP, 200 nM DNA forward primer and 1x Q5 reaction buffer in 25 µL reaction volume. A one step cycling protocol was chosen where denaturation at 98°C for 1 min, annealing at 62°C for 45 s and finale extension at 72°C for 2 min were conducted. Buffer NTI (Macherey-Nagel) was mixed with water in ratio of 3:1 and 50 µL NTI-mix was added to the PCR reaction mix. The NucleoSpin Gel and PCR clean‑up XS kit (Macherey-Nagel) was used for purification and 16 µL elution buffer (Macherey-Nagel) was added for elution. Concentration of the DNA was determined with a qPCR approach described in the chapter above. DNA was repaired by using 0.05 µL PreCR mix (NEB), 1x NAD+, 100 µM of each dNTP, 56.008 fM DNA and 1x ThermoPol reaction buffer (NEB) to reach 11.25 µL end volume. After reaction for 20 min at 37°C, DNA mix was directly used for Amplicon PCR with NEBNext Ultra II Q5 Master Mix (NEB) as described in the chapter above (final DNA concentration 22 fM). Purification of DNA was performed by agarose gel electrophoresis (2.5 % agarose gel in 1x TAE buffer), excision of the respective bands and applying the NucleoSpin Gel and PCR clean-up XS kit (Macherey-Nagel). Here, buffer NTI (Macherey-Nagel) was diluted with Milli-Q water in ration 2:1 and 450 µL NTI mix was added to the gel pieces. After complete dissolving at 50°C, mixture was dilute once again with Milli‑Q water to reach a final volume of 1750 µL. DNA was loaded on the column and eluted with 20 µL elution buffer (Macherey-Nagel). DNA Repair on the whole eluate and purification with the QIAEX II system (Qiagen) was performed as described in the chapter above. The concentration of the final DNA library was determined by Quantus™ Fluorometer (Promega) and usually ranged between 6 and 46 nM. After quality control with Bioanalyzer 2100 (Agilent), DNA libraries were pooled and sequenced in paired-end mode (2*75 bp) on an IIlumina NextSeq2000 instrument.

tag: protocol

value: unmodified RNA; RT by RT-KTq I614Y with 100 µM d(G/C/T)TP & 2 µM dATP

tag: molecule type

value: 40 nt RNA oligonucleotide


title: Ψ-modified RNA oligo designed from human 18S rRNA - RT-KTq - 2µMdATP

status: Public on Mar 15 2023

type: SRA

country: Germany

library_source: other

molecule: other

value: Ψ-modified RNA; RT by RT-KTq with 100 µM d(G/C/T)TP & 2 µM dATP


title: Ψ-modified RNA oligo used in screening - RT-KTq - 2µMdATP

source_name: chemically synthesized oligo

value: 53 nt RNA oligonucleotide


title: unmodified RNA oligo used in screening - RT-KTq I614Y - 2µMdATP


title: Ψ-modified RNA oligo designed from human 18S rRNA - RT-KTq I614Y - 2µMdATP

value: Ψ-modified RNA; RT by RT-KTq I614Y with 100 µM d(G/C/T)TP & 2 µM dATP


title: Ψ-modified RNA oligo used in screening - RT-KTq I614Y - 2µMdATP


title: Ψ-modified RNA oligo used in screening - RT-KTq I614Y - 100µMdATP

value: Ψ-modified RNA; RT by RT-KTq I614Y with 100 µM dNTP


title: Ψ-modified RNA oligo used in screening - RT-KTq - 100µMdATP

value: Ψ-modified RNA; RT by RT-KTq with 100 µM dNTP


title: unmodified RNA oligo used in screening - RT-KTq I614Y - 100µMdATP

value: unmodified RNA; RT by RT-KTq I614Y with 100 µM dNTP


title: unmodified RNA oligo used in screening - RT-KTq - 100µMdATP

value: unmodified RNA; RT by RT-KTq with 100 µM dNTP


title: ST_AN_K-365

city: Boston

first: Adam

last: Labadorf

state: MA

address: 72 East Concord Street E301

department: Neurology

country: USA

institute: Boston University Medical School

library_source: transcriptomic

data_processing:
Read library quality was assessed using FastQC and multiQC
Illumina adapters were removed and leading and trailing low quality bases (below quality 30) were trimmed using trimmomatic
Reads less than 36 bases long after trimming were dropped.
Genome and Annotation (GTF) were from GENCODE v38.  Trimmed reads were then aligned directly to the contiguous splice graphs built from the hg38 human reference genome with STAR.
Used HTSeq counts for quantification
Genome_build: hg38
Supplementary_files_format_and_content: comma separated gene counts file

molecule: polyA RNA

organism: Homo sapiens

source_name: prefrontal cortex (BA9)

extract_protocol: RNA isolation protocol by BU core

tag: tissue

value: prefrontal cortex (BA9)

tag: age

tag: rin

tag: apoe


title: barcode_splice_site_association (MPSA)

city: Cold Spring Harbor

first: Carlos

last: Martí-Gómez

email: carlos199m1@gmail.com, martigo@cshl.edu

state: New York

address: 1 Bungtown Rd

department: Quantitative Biology

institute: Cold Spring Harbor Laboratory

data_processing:
Each barcode was computationally associated with its corresponding 5’ss, and the total number of reads for each 5’ss was tallied: ninc and ntot
A relative splicing ratio was then computed as r = (ninc/ntot)/(Ninc/Ntot), where Ninc and Ntot denote the total number of reads in the inclusion RNA and total RNA samples
Supplementary files format and content: csv files for each sequence context with estimated PSIs per biological replicate
Library strategy: Amplicon sequencing

source_name: synthetic construct

growth_protocol: HeLa cells were seeded at 5x10^5 cells on 150 mm plates, cultured under 37C 5% CO2 for 24 hrs, applied drug treatment and further cultured for 48 hours.

extract_protocol:
Total RNA was extracted by Trizol following the manufacturer's protocol. Plasmids containing barcode-association were extracted by MaxiPrep using PureLink HiPure Plasmid filter Maxiprep kit (ThermoFisher). Then a fraction of them were applied for Illumina adapter ligation and pair-end sequencing
A second round of amplification of the inclusion and total products added Illumina-compatible ends for sequencing

treatment_protocol: HeLa cells were treated with 100 nM risdiplam, 50 nM branaplam, or solvent DMSO.

tag: cell line

value: does not correspond to any biological sample

tag: product

tag: treatment


title: unmodified RNA oligo designed from human 18S rRNA - RT-KTq - 2µMdATP

value: unmodified RNA; RT by RT-KTq with 100 µM d(G/C/T)TP & 2 µM dATP


title: unmodified RNA oligo used in screening - RT-KTq - 2µMdATP


title: ST-T10-470 GRP ST-2 ONE DAY [STD-T10-470]

type: RNA

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

hyb_protocol: cRNA was hybridized to a whole mouse genome microarray (Agilent Technologies) following manufacturer's instructions

scan_protocol: Scanned on a Agilent Technologies Scanner G2600D Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and GeneSpring v.10.1 (Agilent Technologies, Inc., CA) software was used to conduct the preliminary data filtration and statistical analysis.

molecule: total RNA

organism: Mus musculus

source_name: Agilent's Universal Mouse Reference RNA composed of total RNA from 11 mouse cell lines

label_protocol: Total RNA (200-2000ng) was used as starting material, which was amplified using the Quick Amp Two-Color Kit (Agilent Technologies).The labelled cDNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: growth protocol is not applicable

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Three groups of C57BL/6j mice of 3 weeks age were introduced to one of the diet types for the subsequent 24 weeks

tag: gender

value: Male

tag: diet

value: Unknown

source_name: Hemibrain

tag: strain

value: standard lab diet (STD, n3:n6= 1:6)


title: ST-C10-469 GRP ST-2 CONTROL [STD-C10-469]


title: ST-C10-468 GRP ST-2 CONTROL [STD-C10-468]


title: ST-C10-466 GRP ST-2 CONTROL [STD-C10-466]


title: ST-C10-465 GRP ST-2 CONTROL [STD-C10-465]


title: ST-C10-437 GRP ST-1 CONTROL [STD-C10-437]


title: ST-T10-441 GRP ST-1 SIX WEEKS [STD-T10-441]


title: ST-T10-474 GRP ST-2 ONE DAY [STD-T10-474]


title: ST-C10-467 GRP ST-2 CONTROL [STD-C10-467]


title: ST-T10-472 GRP ST-2 ONE DAY [STD-T10-472]


title: ST-T10-471 GRP ST-2 ONE DAY [STD-T10-471]


title: ST-T10-473 GRP ST-2 ONE DAY [STD-T10-473]


title: ST-T10-438 GRP ST-1 SIX WEEKS [STD-T10-438]


title: 58-T10-463 GRP 58-2 ONE DAY [BLD-T10-463]

value: n-3 PUFA optimally balanced by n-6 PUFA (BLD, n3:n6= 1:1)


title: ST-C10-435 GRP ST-1 CONTROL [STD-C10-435]


title: 58-C10-458 GRP 58-2 CONTROL [BLD-C10-458]


title: ST-T10-442 GRP ST-1 SIX WEEKS [STD-T10-442]


title: 58-T10-460 GRP 58-2 ONE DAY [BLD-T10-460]


title: ST-T10-439 GRP ST-1 SIX WEEKS [STD-T10-439]


title: BMDC LPS + ATP Biol Rep 3

city: New Orleans

first: James

last: McLachlan

state: Louisiana

address: 1430 Tulane Ave.

department: Microbiology & Immunology

institute: Tulane School of Medicine

data_processing:
FASTQ data were generated by Illumina Basespace.
Sequencing reads were annotated and aligned to the UCSC mouse reference genome (GRCm38/mm10) using RNA-seq Aligner STAR
Functional analysis was performed on differentially expressed genes in each time point and were uploaded and analyzed separately using the software package IPA (Ingenuity Systems, Redwood City, CA, USA). The resulting biological functions, canonical pathways, and upstream regulators were filtered by setting a threshold of P < 0.05 using Fisher’s exact test.
Supplementary files format and content: Microsoft Excel file of compiled comparison of all gene expression abunddnace between treatments
Supplementary files format and content: Microsoft Excel file of IPA pathway analysis between groups

source_name: Bone marrow

growth_protocol: BMDCs from C57BL/6 mice were cultured from femur bone marrow using GMCSF

extract_protocol:
Total RNA was extracted from lung tissue according to RNeasy Plus Mini Kit protocol from QIAGEN.
Library construction was performed according to TruSeq mRNA protocol from Illumina

treatment_protocol: BMDCs were treated for 24 hours with the adjuvants dmLT, MPL-A, and the combination thereof and then induced gene expression in BMDCs was compared between groups

value: Bone marrow

tag: cell type

value: Dendritic cell

tag: genotype

value: WT

value: LPS + ATP


title: ST-C10-436 GRP ST-1 CONTROL [STD-C10-436]


title: ST-C10-434 GRP ST-1 CONTROL [STD-C10-434]


title: BMDC LPS + ATP Biol Rep 2


title: 58-C10-457 GRP 58-2 CONTROL [BLD-C10-457]


title: BMDC dmLT + MPL-A Biol Rep 1

value: dmLT + MPL-A


title: BMDC LPS + ATP Biol Rep 1


title: ST-C10-433 GRP ST-1 CONTROL [STD-C10-433]


title: ST-T10-440 GRP ST-1 SIX WEEKS [STD-T10-440]


title: 58-T10-461 GRP 58-2 ONE DAY [BLD-T10-461]


title: BMDC MPL-A Biol Rep 2

value: MPL-A


title: BMDC dmLT + MPL-A Biol Rep 3


title: BMDC MPL-A Biol Rep 1


title: BMDC dmLT Biol Rep 3

value: dmLT


title: BMDC dmLT + MPL-A Biol Rep 2


title: 58-C10-455 GRP 58-2 CONTROL [BLD-C10-455]


title: 58-T10-428 GRP 58-1 SIX WEEKS [BLD-T10-428]


title: 58-C10-459 GRP 58-2 CONTROL [BLD-C10-459]


title: 58-T10-444 GRP 58-1 SIX WEEKS [BLD-T10-444]


title: 58-T10-462 GRP 58-2 ONE DAY [BLD-T10-462]


title: BMDC dmLT Biol Rep 2


title: 58-C10-456 GRP 58-2 CONTROL [BLD-C10-456]


title: BMDC dmLT Biol Rep 1


title: 58-C10-425 GRP 58-1 CONTROL [BLD-C10-425]


title: BMDC MPL-A Biol Rep 3


title: BMDC Untreated Biol Rep 2

value: Untreated


title: BMDC Untreated Biol Rep 1


title: 58-T10-431 GRP 58-1 SIX WEEKS [BLD-T10-431]


title: 58-T10-432 GRP 58-1 SIX WEEKS [BLD-T10-432]


title: BMDC Untreated Biol Rep 3


title: 58-C10-426 GRP 58-1 CONTROL [BLD-C10-426]


title: 58-T10-430 GRP 58-1 SIX WEEKS [BLD-T10-430]


title: 58-C10-424 GRP 58-1 CONTROL [BLD-C10-424]


title: ST_AN_K-379


title: T47D E2 Rep1

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

data_processing:
Reads were processed using cutadapt with parameters -a TGGAATTCTCGGGTGCCAAGG --cut 7 --length 42 -m 21.
Reverse complement sequences were generated using fastx_reverse_complement from the FASTX toolkit (v 0.0.13).
Reads were aligned to hg19 with bowtie2 in end-to-end mode, and non-uniquely aligned reads were discarded.
Bam files were converted to bed format using bedtools bamToBed. Alignments on the positive and negative strands were separated before being converted to bedgraph using bedtools genomeCoverageBed (v2.28.0).
Bedgraphs were converted to biwgwig using bedGraphToBigWig v 4
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: PRO-seq

growth_protocol: PRO-seq libraries were generated as described in Mahat et al., 2016. Briefly, Ishikawa and T-47D cells were grown in hormone-depleted RPMI for five days, then 2x106 cells were plated into two 10 cm dishes per condition with RPMI lacking phenol red supplemented with 10% charcoal/dextran-stripped FBS and penicillin.

extract_protocol:
Cells were permeabilized for five minutes with permeabilization buffer [10 mM Tris-HCl, pH 7.4; 300 mM sucrose; 10 mM KCl; 5 mM MgCl2; 1 mM EGTA; 0.05% Tween-20; 0.1% NP40 substitute; 0.5 mM DTT, protease inhibitor cocktail ml(Roche); and SUPERaseIn RNase Inhibitor (Ambion)]. The nuclear run-on was performed by adding permeabilized cells to run-on mixture [final composition was 5 mM Tris, pH 8.0; 25 mM MgCl2; 0.5 mM DTT; 150 mM KCl; 200 μM rATP; 200 μM rGTP; 20 μM biotin-11-rCTP (Perkins Elmer); 20 μM biotin-11-rUTP (Perkins Elmer); 1 U/μL SUPERase In RNase Inhibitor (Ambion); 0.5% Sarkosyl], then incubating at 37°C for 5 minutes. RNA was extracted with Trizol LS (Ambion), fragmented with 0.2 N NaOH for 8 minutes on ice, then neutralized with 0.5 M Tris, pH 6.8, followed by buffer exchange with a P-30 column (Bio-Rad). Biotinylated RNAs were enriched with Dynabeads M280 Streptavidin (Invitrogen), then RNA was extracted with Trizol (Ambion),
3′ adapters were ligated using T4 RNA ligase (NEB). Biotinylated RNAs were enriched for a second time, followed by 5′ cap repair with RppH (NEB) and 5′ hydroxyl repair with PNK (NEB). The 5′ adapter was ligated with T4 RNA ligase (NEB), followed by a third biotinylated RNA enrichment. Reverse transcription was performed with the RP1 primer. Samples were PCR amplified for 13 cycles, then cleaned up with Agencourt AMPure XP beads (Beckman Coulter)

treatment_protocol: Cells were treated with vehicle (DMSO) or 10 nM 17beta-estradiol (E2) for 45 minutes

value: Breast; Ductal Carcinoma

value: 10nM E2


title: T47D E2 Rep2


title: 57-T10-454 GRP 57-2 ONE DAY [ERD-T10-454]

value: high n-3 PUFA enriched diet (ERD n3:n6= 7:1)


title: 58-C10-443 GRP 58-1 CONTROL [BLD-C10-443]


title: 57-T10-452 GRP 57-2 ONE DAY [ERD-T10-452]


title: 58-C10-423 GRP 58-1 CONTROL [BLD-C10-423]


title: 57-T10-451 GRP 57-2 ONE DAY [ERD-T10-451]


title: 57-T10-453 GRP 57-2 ONE DAY [ERD-T10-453]


title: Ishikawa DMSO Rep2

source_name: Ishikawa

value: Ishikawa

value: Endometrial Adenocarcinoma

value: DMSO (veh)


title: 57-C10-448 GRP 57-2 CONTROL [ERD-C10-448]

value: Male

value: Unknown


title: Ishikawa E2 Rep2


title: T47D DMSO Rep1


title: ST_AN_K-397

value: prefrontal cortex (BA9)


title: Ishikawa DMSO Rep1


title: Ishikawa E2 Rep1


title: 57-C10-447 GRP 57-2 CONTROL [ERD-C10-447]


title: T-47D H3K27ac HiChIP

description: HiChIP

library_source: genomic

data_processing:
Reads were aligned to human hg19 reference genome using HiC-Pro
Hichipper was used to perform restriction site bias-aware modeling of the output from HiC-Pro and to call interaction loops.
In Ishikawa cells, DMSO and E2 treated HiChIP loops were combined to identify all possible putative enhancers and in LNCaP cells, loops from separate replicates were combined.
Loops with less than 3 counts were removed
Assembly: hg19
Supplementary files format and content: bedpe files
Library strategy: HiChIP

molecule: genomic DNA

growth_protocol: T-47D and Ishikawa cells were cultured in RPMI 1640 medium (Gibco) with 10% fetal bovine serum (Gibco) and 1% penicillin–streptomycin (Gibco). LNCaP cells were cultured in RPMI media with 10% FBS supplemented. Cells were incubated at 37°C with 5% CO2.

extract_protocol:
Cells were pelleted, then resuspended and fixed in 1% formaldehyde for 10 minutes. Cells were then treated with 125 mM glycine for 5 minutes to stop crosslinking.
HiChIP and library construction was performed as described in Mumbach et al. Nature Methods 2016 (see supplementary protocol) with the following modifications: Ishikawa cells were digested with restriction enzyme DpnII. Crosslinked chromatin from Ishikawa cells was sonicated using an EpiShear probe-in sonicator (Active Motif) with three cycles of 30 seconds at an amplitude of 40% with 30 seconds rest between cycles. Crosslinked chromatin from T-47D and LNCaP cells was sonicated using Covaris E220 with the settings of fill level=10, duty cycle=5, PIP=140, cycles per burst=200, time=4 mins.

treatment_protocol: Ishikawa cells were treated with either 10 nM 17beta-estradiol (E2) for 1 hour or DMSO as a vehicle control.

tag: hichip antibody

value: H3K27ac (Abcam ab4729)

tag: restriction enzyme

value: MboI (New England Biolabs)


title: LNCaP H3K27ac HiChIP_rep2

description: HiChIP

source_name: LNCaP

value: LNCaP

value: Prostate Carcinoma


title: 57-C10-445 GRP 57-2 CONTROL [ERD-C10-445]


title: 57-T10-450 GRP 57-2 ONE DAY [ERD-T10-450]


title: 57-C10-446 GRP 57-2 CONTROL [ERD-C10-446]


title: 57-T10-422 GRP 57-1 SIX WEEKS [ERD-T10-422]


title: T-47D Pol2 E2 Rep2

data_processing:
ChIP-seq reads were aligned to hg19 using bowtie v1.1.2 with parameters -m 1 –t –best -q -S -l 32 -e 80 -n 2
Peaks were called using macs2 V 2.1.0.20140616 with the following arguments: macs2 callpeak -B --SPMR --pvalue=1e-10 --mfold 15 100.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: RPMI 1640 medium (Gibco) with 10% fetal bovine serum (Gibco) and 1% penicillin–streptomycin (Gibco)

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes at room temperature and then treated with 125 mM Glycine for 5 minutes to stop crosslinking. Crosslinked cells were then washed with cold PBS and scraped to harvest.
ChIP and library construction was performed as described in Reddy et al, Genome Research, 2009.

treatment_protocol: Cells were treated with vehicle (DMSO) or 17beta-estradiol (E2) at a final concentration of 10nM for either 1 hour for transcription factor ChIP-seqs, or 8 hours for histone marker ChIP-seqs

tag: chip antibody

value: RNA polymerase II CTD repeat YSPTSPS (Abcam ab5408)

value: 10 nM 17beta-estradiol

tag: time

value: 1 hour


title: T-47D Input Single-end

value: none (input)


title: LNCaP H3K27ac HiChIP_rep1

description: HiChIP


title: T-47D Pol2 DMSO Rep2

value: Breast; Ductal Carcinoma


title: T-47D SIN3A Full Media

value: SIN3A (described in Hassig et al. Cell 2017)

value: Full RPMI


title: T-47D Pol2 E2 Rep1


title: 57-T10-419 GRP 57-1 SIX WEEKS [ERD-T10-419]

value: high n-3 PUFA enriched diet (ERD n3:n6= 7:1)


title: 57-C10-417 GRP 57-1 CONTROL [ERD-C10-417]


title: 57-T10-420 GRP 57-1 SIX WEEKS [ERD-T10-420]


title: 57-C10-414 GRP 57-1 CONTROL [ERD-C10-414  ]


title: 57-C10-415 GRP 57-1 CONTROL [ERD-C10-415]


title: RB355_Etop, INPP4B, rep3

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

institute: University Hospital Essen

data_processing:
Sequences were trimmed with TrimGalore and standard settings
Sequences were aligned with hisat2 (standard settings) on grcm38
Reads were counted by summarizeOverlaps
Assembly: grcm38
Supplementary files format and content: semicolon separated file contains the raw transcript counts

source_name: retinoblastoma

extract_protocol:
miRNeasy Kit (Qiagen, Hilden, Germany)
Libraries were construced with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD

value: retinoblastoma

value: etoposide resistant

tag: vector

value: INPP4B overexpression


title: 57-T10-418 GRP 57-1 SIX WEEKS [ERD-T10-418]

value: Male

value: Unknown


title: RB355_Etop, INPP4B, rep2


title: RB355_Etop, INPP4B, rep1


title: RB355_Etop, control, rep3

value: empty vector control


title: T-47D SIN3A Stripped Media

value: Charcoal Stripped Media


title: Ishikawa Input Single-end

value: Ishikawa

value: Endometrial Adenocarcinoma


title: Ishikawa H3K36me3

value: H3K36me3 (Abcam ab9050)

value: 8 hour


title: Ishikawa SIN3A Full Media

value: 1 hour


title: Y79_Etop, INPP4B, rep2


title: RB355_Etop, control, rep2


title: Y79_Etop, INPP4B, rep3


title: ALDH1 high

city: Beijing

first: Ling-fei

last: Jia

address: 22 Zhongguancun Avenue South, Haidian District

country: China

institute: Peking University School and Hospital of Stomatology

description: extracting RNA after  isolated by flow cytometry based on ALDEFLUOR analysis

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Transcripts per million(TPM) were calculated using RSEM(1.1.21) with parameters(-p 8 --estimated-rspd --no-bam-output).
Assembly: GRCh38
Supplementary files format and content: xls files including RPKM values for each RNA-seq samples.

extract_protocol:
Total RNA was extracted using Trizol
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

value: tumor cell lines

tag: passage


title: Ishikawa SIN3A Stripped Media


title: T-47D Pol2 DMSO Rep1

value: Breast; Ductal Carcinoma

value: RNA polymerase II CTD repeat YSPTSPS (Abcam ab5408)

value: DMSO (veh)


title: Y79_Etop, INPP4B, rep1


title: ALDH1 low


title: Y79_Etop, control, rep2


title: SUIT2_ChIP_R2

city: Seattle

first: Matt

last: Fitzgibbon

state: Washington

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

data_processing:
Basecalling and demultiplexing were performed with Illumina bcl2fastq 1.8.4
ChIP-seq reads were aligned to the human hg19 genome using Bowtie v1.1.1
Peaks were called with MACS2 using narrow peak, paired-end mode
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including peaks called by MACS2

source_name: SUIT2 cells

growth_protocol: Human PDA cells were grown under standard culture conditions

extract_protocol:
Cells were croslinked with 1% paraformaldehyde, sonicated and soluble chromatin were isolated with antibody
ChIP-seq libraries were prepared with the KAPA HyperPrep kit (Roche).

treatment_protocol: no treatment

value: SUIT2 cells


title: SUIT2_ChIP_R1


title: RB355_Etop, control, rep1

value: retinoblastoma


title: Y79_Etop, control, rep1

value: etoposide resistant


title: Panc327_Input_R2

source_name: Panc327 cells

value: Panc327 cells


title: Panc327_Input_R1


title: RNA_hESC,rep3

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

data_processing:
Fastq files were mapped to the hg19 reference using bowtie
Bigwig coverage tracks were generated using deepTools bamCoverage [version 3.4.1]
Coverage peaks were called using MACS [version 2.1.2]
Tommy, explain how the FPKM file was created?
Assembly: hg19
Supplementary files format and content: coverage bigwig file for each sample. A tab-delimited text file with FPKM values for all sample

source_name: Humna embryonic stem cells H9 (WA09)

growth_protocol: We used H9.1 human pluripotent stem cells (hPSCs) that are grown on inactivated mouse embryonic fibroblasts (MEFs) in 6 well plate supplemented with human PSC medium (hPSCM) composed of DMEM/F12 (Gibco cat. 11330, USA), 1% non-essential amino acids (Gibco cat. 11140, USA), 1% GlutaMAX (Gibco cat. 35050, USA), 2-mercaptoethanol (Sigma-Aldrich cat.M3148, USA), knockout serum replacement (Gibco cat. 10828, USA) with 4ng/ml Fibroblast growth factor 2 (FGF2) (Invitrogen cat.13256-029, USA). The hPSCs first are induced into neural stem cells in the first 10 days then the cells are patterned into ventral forebrain progenitors with MGE characteristic. The hPSC are dissociated using TrypLE (Gibco cat. 12604021, USA.)  and transfer to 10mm plate in suspension and grown hPSCM without Fibroblast growth factor 2 (FGF2) at the first 24h 10uM rock inhibitor (y27632, STEMCELL cat. 129830-38-2, canada) was used, the two third of medium was removed and replaced by new medium every day. The hPSC are becoming embryonic bodies (EBs) at the first day which are spheres that are in suspension. At day 4, the medium was aspirated and replaced with neural induction medium (NIM) that contain DMEM/F12, 1% non-essential amino acids, 1% N-2 supplement (Gibco cat. 17502-048, USA) and heparin (Sigma-Aldrich cat.H3149, USA) and was incubated additional three days while replacing the medium every other day. At day 7, the EBs are plated in 6 well plate that is coated with laminin (Invitrogen cat.23017-015, USA) in order to facilitate the attachment of the EBs, 35–50 EBs per well were plated, NIM was replaced every other day. Neural rosettes appear at day 10, which is the end of the first stage. Neural rosettes were cultured with NIM containing 1.5 μM Pur (SHH agonists) (StemGent cat.04-0009, USA) and was replaced every other. At day 16, the colonies of the neural rosettes were gently detached and moved to 10 mm plate, the lifted neural rosettes were cultured with NIM containing Pur and B27(Gibco cat. 12587-010, USA) the medium was changed every other day till day 25 which is the end of the second stage. On day 26, MGE progenitor spheres were collected and gently pipetted for 3-4 times to disassociate the cells. Then, the cells were plated on poly-l-ornithine (PLO) (Sigma-Aldrich cat.P3655,USA)and laminin-coated coverslips. MGE cells usually attach to the coverslip after 3–4 h. After 4 h neural differentiation medium (NDM) comprised of neuralbasal medium (Gibco cat. 21103, USA) 1% non-essential amino acids, 1% N-2 supplement containing 1 μM cAMP(Sigma-Aldrich cat.D-0260,USA, 10 ng ml−1 BDNF (Gibco cat. PHC7074, USA), 10 ng ml−1 GDNF (Gibco cat. PHC7044, USA), 10 ng/ml IGF1 (PeproTech cat.100-11, USA) and compound E (EMD Biosciences cat. 565790-500UG) was added to each well. The medium was replaced every 3 days, but without adding compound E which is only added once in order to synchronize cell differentiation. Then, the cells are differentiated and cultured till day 55. In the third stage the progenitors are differentiated to GABAergic-like interneurons by day 39. In long-term culture at day 55 we can get population of neurons that expressed somatostatin (SST) neurotransmitter.

extract_protocol:
RNA extracted using total RNA purification micro kit (Norgen cat.35300, Canada). the lysate was treated on column with DNase I to remove DNA contamination. RNA was extracted from the four developmental stage: Day 0 (hESC), Day 26, Day 39, Day 55 in replicates and libraries were prepared by illumine kits.
Illumina Stranded mRNA Prep

value: Humna embryonic stem cells H9 (WA09)


title: RNA_hESC,rep2


title: Panc327_ChIP_R1


title: RNA_hESC,rep1


title: RNA_Day55,rep3

source_name: Mature Somatosatin expressed interneuron-like cells

value: Day 55


title: BxPC3_Input_R2

source_name: BxPC3 cells

value: BxPC3 cells


title: BxPC3_Input_R1


title: Panc327_ChIP_R2


title: 57-T10-421 GRP 57-1 SIX WEEKS [ERD-T10-421]

value: Male

value: Unknown

value: high n-3 PUFA enriched diet (ERD n3:n6= 7:1)


title: RNA_Day39,rep2

source_name: Mature interneuron-like cells

value: Mature interneuron-like cells

value: Day 39


title: RNA_Day55,rep1

value: Mature Somatosatin expressed interneuron-like cells


title: RNA_Day39,rep1


title: BxPC3_ChIP_R2


title: Y79_Etop, control, rep3

value: empty vector control


title: RNA_Day55,rep2


title: SUIT2_Input_R2


title: BxPC3_ChIP_R1


title: RNA_Day26,rep1

source_name: Interneuron-like progenitors

value: Interneuron-like progenitors

value: Day 26


title: SUIT2_Input_R1


title: SUIT2 cells THZ1 treated rep1

data_processing:
Basecalling and demultiplexing were performed with Illumina bcl2fastq 1.8.4
RNA-seq reads were aligned to the human hg38 genome assembly using TopHat v2.1.0
Per-gene counts were determined using HTSeq v0.6.1
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files including raw counts assigned to each gene for each sample

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation v2 kit (Illumina)

treatment_protocol: 100nM THZ1 or DMSO control for 6hrs


title: SUIT2 cells THZ1 treated rep2


title: ATAC_d26

data_processing:
Fastq files were mapped to the hg19 reference using bowtie
Bigwig coverage tracks were generated using deepTools bamCoverage [version 3.4.1]
Coverage peaks were called using MACS [version 2.1.2]
Assembly: hg19
Supplementary files format and content: bigwig generated using deepTools
Supplementary files format and content: bed generated using MACS2

source_name: MGE-like progenitors

extract_protocol:
The samples were purified using Qiagen MiniElute kit (QIAGEN, 28204), Transposed fragments were directly PCR amplified and sequenced on an Illumina NextSeq 500 platform to generate 2 ×36-bp paired-end reads.
ATAC-seq library preparation was performed as previously described (Buenrostro et al., 2013). Briefly, cells were trypsinized and 50,000 cells were counted and incubated in lysis buffer to isolate nuclei. Nuclei were then resuspended in transposase reaction mix for 30 min at 37 °C (Illumina, Fc-121-1030).

tag: days from treatment


title: SUIT2 cells DMSO treated rep2

value: DMSO


title: ATAC_d39

source_name: GABAergic-like interneurons


title: SUIT2 cells DMSO treated rep1

value: SUIT2 cells


title: H3K27ac_d55

source_name: GABAergic-like mature interneurons

extract_protocol:
DNA was extracted using AMPure XP beads (Beckman Coulter Genomics, A63881). Chip sample libraries were prepared according to Illumina Genomic DNA protocol as described (Mikkelsen et al., 2007).
Chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq) is a method used to analyze protein interactions with DNA. ChIP-seq combines with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. 106 of differentiated cells from Day 26, Day 39, Day 55 stages were cross-linked using 1% formaldehyde. The lysate with sodium dodecyl sulfate-based reagents, and chromatin was sonicated for 18 cycles of (60 sec On, 60 sec Off)  using Bioruptor 208.The sonicated samples were immunoprecipitated using magnetic beads 25ul protein A (Invitrogen cat.10002D) and 25ul protein G (Invitrogen cat.10004D). The samples were reverse crosslinked using Proteinase K overnight at 650C. The sonicated fragments were 300-500bp size. The DNA fragments were purified using phenol-chloroform protocol209. ChIP was performed using antibodies against H3K27ac (Abcam Ab4729) and H3K27me3 (Abcam Ab4729). To verify the quality of experiment, ChIP samples were taken to qPCR with primers for positive and negative controls (table 6).  Prepared libraries from ChIP and input DNA were sequenced using HiSeq instrument (Illumina, USA). the ChIP libraries were analyzed and mapped to hg19 using BWA 210 and peaks were called using MACS211.

tag: chip-seq antybody


title: healthy volunteers 5 miRNA

city: zhengzhou

first: Yao

last: Lu

state: henan province

address: 1 Jianshe Dong Lu, Zhengzhou City, Henan Province, China

institute: zhengzhou university

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8
Sequencing quality are examined by FastQC and trimmed reads (trimmed 5‘,3’-adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature tRNA sequences
reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie
Raw reads were normalized by calculated CPM value
Assembly: hg19
Supplementary files format and content: The xlsx format file contains the CPM value of gene in every sample

source_name: intestinal tissue

extract_protocol:
Total RNA was extracted from vitreous humour using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).Total RNA was pretreated to remove  some modification which interfere with small RNA-seq library construction(e.g. m1A).
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 134-160 bp PCR amplified fragments (corresponding to 14-40 nt small RNAs).

tag: tissue

value: intestinal tissue


title: Panc327 cells THZ1 treated rep3

tag: cell line


title: RNA_Day26,rep2


title: H3K27ac_d39


title: healthy volunteers 4 miRNA


title: Panc327 cells THZ1 treated rep1


title: H3K27ac_d26


title: Panc327 cells DMSO treated rep3


title: Panc327 cells THZ1 treated rep2


title: healthy volunteers 2 miRNA


title: Panc327 cells DMSO treated rep2


title: Panc327 cells DMSO treated rep1


title: H3K27me3_d26


title: IBS-D patient 5 miRNA


title: SUIT2 cells THZ1 treated rep3


title: healthy volunteers 1 miRNA


title: healthy volunteers 3 miRNA


title: BxPC3 cells THZ1 treated rep3


title: 57-C10-413 GRP 57-1 CONTROL [ERD-C10-413  ]

source_name: Agilent's Universal Mouse Reference RNA composed of total RNA from 11 mouse cell lines


title: IBS-D patient 4 miRNA


title: BxPC3 cells THZ1 treated rep2


title: IBS-D patient 3 miRNA


title: BxPC3 cells THZ1 treated rep1


title: SUIT2 cells DMSO treated rep3


title: IBS-D patient 2 miRNA


title: BxPC3 cells DMSO treated rep3


title: NOX4 KO TGFb2 rep3

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.96
Supplementary_files_format_and_content: Raw counts measurements

source_name: Primary skin mouse fibroblasts

growth_protocol: Primary skin fibroblasts were cultured in complete DMEM medium suplemented with 10% FBS, 1% P/S

extract_protocol:
RNA was extracted using RNAeasy Mini kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary skin fibroblasts were passaged and plated in desired density, after 24h cells were starved for another 24h, and then stimulated with 10ng/ml TGF-beta 2 for 24h

value: Skin

value: NOX4 KO

tag: stimulation

value: 10 ng/ml TGF-beta 2; 24h


title: BxPC3 cells DMSO treated rep2

tag: treatment


title: BxPC3 cells DMSO treated rep1


title: D3-MDMs uninfected Donor 4

city: Botucatu

first: Geysson Javier

middle: Fernandez

last: Garcia

state: Sao Paulo

address: Departamento morfologia IBB UNESPRubiao Junior

country: Brazil

institute: UNESP

data_processing:
Sequenced reads were performed quality assessment using FastQC. Reads with phred score >30 were accepted
Adapters were removed using trimomatic in the default options
Single-end reads for mRNA were mapped to the GRCh38.p13 genome using STAR with default options
Counts for RefSeq genes were obtained using Featurecounts with the default settings
DESeq2 was used to normalize expression counts.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: monocyte-derived macrophages

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) from blood samples of 4 healthy donors mixed with 2% EDTA, were isolated through density gradient with Lymphoprep. Monocytes were obtained from total PBMCs by adherence to the plastic and differentiation to macrophages was allowed to occur for 6 days in RPMI-1640 medium supplemented with 10% (v/v) FBS, 4 mM L-glutamine, 0.3% (v/v) NaCO3, and 1% (v/v) antibiotic-antimycotic solution 100X (complete medium), at 37 °C and 5% CO2, without growth factors

extract_protocol:
Total RNA  was obtained using Direct-zol ™ RNA Miniprep Plus (Zymo Research, Irvine, California) following the manufacturer’s protocol. RNA samples were treated with DNase I column (Zymo Research, Irvine, California) to remove contaminating genomic DNA. RNA was quantifed, and the quality of each RNA sample was checked by spectrophotometry (Thermo Scientifc, Wilmington, DE, USA). Additionally, RNA quality was determined by analysis of ribosomal RNAs, using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).
Libary construction was made using the KAPA Stranded mRNA-Seq Kit (cat #KK8421, KAPA Biosystems, Wilmington, MA)

treatment_protocol: MDMs were differentiated in presence of 1,25 di-hydroxyvitamin D3 to obtain D3-MDM. 1,25 di-hydroxyvitamin D3 was added to the culture media at a final concentration of 1 nM and replenished every 24 h for six days. MDM and D3-MDM monolayers were washed with warm PBS and were infected with  Zika virus strain COL345Si-Asian at MOI of 5. Three hpi, the cells were washed with warm PBS to remove unbound virus. Then 24 hpi, macrophage monolayers were used for sample collection.

value: monocyte-derived macrophages

tag: infection status

value: Uninfected

tag: hours post infection

tag: vitamin d treatment

value: vitamin D treated

tag: donor

value: Donor 4


title: D3-MDMs 24 h infected Donor 4

tag: cell type

value: ZIKV infected


title: Untreated_MDMs uninfected Donor 4

value: untreated


title: Untreated_MDMs 24 h infected Donor 4


title: NOX4 KO TGFb2 rep2

tag: strain

tag: genotype


title: WT CTRL rep 3

value: WT

value: Non


title: D3-MDMs 24 h infected Donor 3

value: Donor 3


title: D3-MDMs uninfected Donor 3


title: NOX4 KO CTRL rep 2


title: Untreated_MDMs 24 h infected Donor 3


title: WT TGFb2 rep 2


title: Untreated_MDMs uninfected Donor 3


title: WT CTRL rep 2


title: Untreated_MDMs 24 h infected Donor 2

value: Donor 2


title: D3-MDMs 24 h infected Donor 2


title: D3-MDMs uninfected Donor 2


title: NOX4 KO TGFb2 rep1


title: WT TGFb2 rep 1


title: NOX4 KO CTRL rep 3


title: WT CTRL rep 1


title: WT TGFb2 rep 3


title: D3-MDMs 24 h infected Donor 1

value: Donor 1


title: RHIN_0053

data_processing:
Trimmed fastqs using Trimmomatic and aligned using STAR v2.7.5a. Aligned reads were counted against Gencode v34 annotation gtf using HTSeq v0.12.4. Genes were filtered from further analysis and differential expression was assessed usingDESeq2 (R v3.6.3, DESeq2 v1.26.0)
Genome_build: gencode v34 primary assembly genome
Supplementary_files_format_and_content: Processed files contain raw counts for all samples

source_name: prefrontal cortex (BA9)

extract_protocol:
QIAzol. Qiagen
Illumina NextSeq, RNA Sample Prep Kit, mRNA

value: prefrontal cortex (BA9)

tag: disease state

value: Chronic Traumatic Encelopathy - repetitive head injury

tag: age at death

tag: rin

tag: total years of play


title: RHIN_0052


title: RHIN_0075


title: RHIN_0028


title: IBS-D patient 1 miRNA

value: intestinal tissue


title: Untreated_MDMs uninfected Donor 2


title: RHIN_0002


title: RHIN_0049


title: D3-MDMs uninfected Donor 1


title: RHIN_0000


title: RHIN_0027


title: CTES_0082

value: Chronic Traumatic Encelopathy - severe


title: CTES_0081


title: RHIN_0001


title: NOX4 KO CTRL rep 1

value: Skin

value: NOX4 KO


title: CTES_0083


title: CTES_0080


title: RHIN_0076


title: T47D DMSO Rep2

value: Breast; Ductal Carcinoma

value: DMSO (veh)


title: CTES_0072


title: Untreated_MDMs uninfected Donor 1

value: monocyte-derived macrophages

value: Uninfected


title: CTES_0068


title: CTES_0073


title: Untreated_MDMs 24 h infected Donor 1

value: ZIKV infected


title: CTES_0071


title: CTES_0067


title: CTES_0066


title: CTES_0065


title: CTES_0062


title: CTES_0064


title: CTES_0060


title: CTES_0059


title: CTES_0057


title: CTES_0079


title: CTES_0055


title: CTES_0048


title: CTES_0042


title: CTES_0063


title: CTES_0041


title: CTES_0040


title: CTES_0037


title: CTES_0036


title: CTES_0035


title: 57-C10-416 GRP 57-1 CONTROL [ERD-C10-416]

tag: gender

value: Male

tag: diet

value: Unknown

source_name: Hemibrain

value: high n-3 PUFA enriched diet (ERD n3:n6= 7:1)


title: CTES_0034

tag: tissue


title: CTES_0033


title: CTES_0024


title: CTES_0032


title: CTES_0030


title: CTES_0022


title: CTES_0061


title: CTES_0023


title: CTES_0047


title: CTES_0018


title: CTES_0056


title: CTES_0016


title: CTES_0014


title: CTES_0046


title: CTES_0015


title: CTES_0038


title: CTES_0039


title: CTES_0012


title: CTES_0010


title: CTES_0011


title: 7d_chd8-/- zebrafish rep2

city: Shanghai

first: Hongji

last: Li

state: Shanghai

address: Building 6, School of Pharmacy, Shanghai Jiao Tong University, No.800 Dongchuan Road, Minhang District, Shanghai

department: School of Pharmacy

institute: Shanghai Jiao Tong University

data_processing:
Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim-galore version 0.6.7 for subsequent analysis with parameters --phred33 -q 20 --length 15 --stringency 3 --fastqc --max_n 3
The processed datas have been mapped to Danio_rerio.GRCz11 whole genome using STAR version 2.7.9a, then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts -T 6 -t exon -g gene_id
Assembly: GRCz11
Supplementary files format and content: Table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: kidney

growth_protocol: The parent adult zebrafish are placed in pair-mating tanks with dividers separating males and females the afternoon or evening prior to mating (Day -1). At the start of the light cycle the following morning (Day 0), the parents were transferred to new clean pair-mating tanks with fish feeding circulation system water and allowed to mate for no more than 1 hour. Fertilized eggs were transfered into petri dishes (less than 100 embryos per dish) with embryo media. Then all of the embryos are incubated at 28.5℃ until the 5 dpf or 7 dpf.  Embryo media:1L ddH2O with 10 ml stock solution A, 1 mL stock solution B, 10 mL stock solution C, 10 mL stock solution D and 10 mL stock solution E, adjust pH to 7.2 with 1 M HCl.(A: 250 mL RO H2O, 20 g NaCl, 1 g KCl;B: 100 mL RO H2O, 0.358 g Na2HPO4 anhydrous, 0.6 g KH2PO4 monobasic;C: 250 mL RO H2O, 4.68 g CaCl2 dihydrate;D: 250 mL RO H2O, 6.15 g MgSO4·7H2O;E: 250 mL RO H2O, 8.75 g NaHCO3).  System water:purified water with sea salt and NaHCO3，conductivity 450-500 μs/cm，pH 7.0±0.2.

extract_protocol:
Intestines and kidneys were removed,immerse the tissues in Trizol reagent immediately, flash frozen in -80℃, and RNA was harvested following the manual of the Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 40 chd8-/- zebrafish embryos at 5 dpf were collected and anesthetized in 0.4% (4g/L) tricane. Then the tricane media were replaced with RNAlater RNA Stabilization Solution (Thermo), and samples were storaged at 4℃ for more than 24h. The intestines were removed and collected by tweezers under the microscope, and the isolated tissue was then transfered into Trizol. About 70 chd8-/- zebrafish embryos at 7 dpf embryos were collected and anesthetized in 0.4% (4g/L) tricane.  Then the media were replaced with RNAlater RNA Solution, and samples were storaged at 4℃ for more than 24h. Their kidneys were removed by tweezers under the microscope. Then the tissues were immersed in Trizol, and the RNA of them were extracted as previously described for intestine tissues.

value: AB

value: kidney

tag: age

value: 7 days after fertilization


title: 7d_chd8-/- zebrafish rep3


title: CTES_0009

value: prefrontal cortex (BA9)


title: CTES_0058


title: CTES_0013


title: CTES_0008


title: 7d_chd8-/- zebrafish rep1


title: 5d_chd8-/- zebrafish rep3

source_name: intestine

value: intestine

value: 5 days after fertilization


title: CTES_0017

value: Chronic Traumatic Encelopathy - severe


title: CTEM_0078

value: Chronic Traumatic Encelopathy - mild


title: CTES_0007


title: CTES_0006


title: 7d_GF zebrafish rep3

growth_protocol: The parent adult zebrafish are placed in pair-mating tanks with dividers separating males and females the afternoon or evening prior to mating (Day -1). At the start of the light cycle the following morning (Day 0), the parents were transferred to new clean pair-mating tanks with autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groups(CV group and GF group).The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media (SEM) and transferred to a petri dish with the filter-sterilized embryo medium containing antibiotics (ABEM). Healthy embryos were sorted into fresh ABEM per 2 hours (less than 200 per dish),and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described (Pham, Kanther et al. 2008). Briefly, embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s, followed with three times rinsing with the SEM at room temperature. After soaking in 0.003% sodium hypochlorite for 16 min at room temperature, these embryos were then washed for three times with the SEM. Finally, the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃.

extract_protocol:
Intestines and kidneys were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% (4g/L) tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution (Thermo), and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope, and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% (4g/L) tricane respectively. Their kidneys were collected as previously described as intestines.

value: germ free


title: 5d_chd8-/- zebrafish rep2


title: CTEM_0077


title: CTEM_0051


title: CTEM_0074


title: 7d_CV zebrafish rep2

value: wild type


title: 7d_GF zebrafish rep1


title: 5d_chd8-/- zebrafish rep1


title: CTEM_0054


title: 7d_CV zebrafish rep3


title: 7d_GF zebrafish rep2


title: CTEM_0050


title: 7d_CV zebrafish rep1


title: CTEM_0031


title: 5d_GF zebrafish rep3


title: CTEM_0026


title: 5d_GF zebrafish rep1


title: CTEM_0029


title: CTEM_0005


title: 5d_CV zebrafish rep1


title: 5d_CV zebrafish rep2


title: 5d_GF zebrafish rep2


title: CTEM_0003


title: CTEM_0025


title: CTEM_0004


title: Donor 3 (64), experience 2 (26), CD4s, TS-CAR (HA)

city: Vancouver

first: Megan

middle: K

last: Levings

address: 950 West 28th Ave

country: Canada

institute: University of British Columbia

data_processing:
Within Illumina BaseSpace RNA-Seq Alignment App (v1.1.0): base-calls made with RTA (v2.1), demultiplexing with bcl2fastq2, read sequences aligned with STAR (v2.5.0a), gene expression quantified as raw counts by Illumina’s RnaReadCounter to generate the processed data files.
From raw counts, DESeq2 (v1.16.1) within R (v.3.4.2) used to identify differentially expressed genes by pairwise comparisons.
GSEAPreranked tool within GSEA software (v3.0) and MSigDB gene set collections (v6.1) used for gene set enrichment analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Per sample: raw counts of all genes, generated by RnaReadCounter

source_name: Peripheral blood naive conventional CD4s

growth_protocol: Naïve Tregs were flow-sorted as live CD4+CD127loCD25hi CD45RA+CD62Lhi cells and naïve CD4+ Tconvs cells were sorted as live CD4+ CD45RA+CD62Lhi. Cells were resuspended at 1x106 cells/ml in XH media (X-Vivo 15 (Lonza) with 5% human serum, 1% penicillin/streptavidin, 1% glutamine and phenol red) containing 300U IL2/ml (Proleukin) and were stimulated with a 3 bead : 1 cell ratio of Dynabead. On day 2 and 3, cells were left untransduced (UT) or transduced with a retrovirus containing a non-tonic signaling CAR (non-TS-CAR; CD19) or a TS one (HA CAR). At day 7, cells were collected and live CAR+ were flow sorted (or live CD4+ for the UT) and resuspended at 0.5x106 cells/ml in XH media containing 300U IL2/ml for an addition 5 days.

extract_protocol:
RNA was extracted from 0.25x106 cells at day 12 of cell culture using the Monarch total RNA miniprep kit (New England Biolabs, T2010S) and quantifies using the Qubit RNA HS Assay kit (Thermo Fisher Scientific, Q32855) according to the manufacturer’s instructions. RNA purity (RNA Integrity Number) was assessed using the RNA 6000 Pico assay (Agilent, 5067-1513)
Qualifying samples (RIN>8) were prepared using the TruSeq stranded mRNA library kit (Illumina) on the Illumina Neoprep automated nanofluidic prep instrument.

treatment_protocol: either left untransduced or transduced with a non-TS CAR (CD19) or a TS one (HA)

tag: independent experiment

tag: cells

value: conventional CD4s

tag: untransduced or car

value: TS-CAR (HA)


title: Donor 3 (64), experience 2 (26), CD4s, non-TS CAR (CD19)

value: non-TS CAR (CD19)


title: Donor 3 (64), experience 2 (26), CD4s, untransduced

value: untransduced


title: 9905.rep2.INPUT

city: Vienna

first: Aleksandra

last: Kornienko

state: Vienna

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

description:
100bp SE
chip.5marks.14accessions.Araport11_PCs_TEs.log2_input_normalized_coverage.80_20_quantiles_normalized.genebody.bed
chip.5marks.14accessions.Araport11_PCs_TEs.log2_input_normalized_coverage.genebody.bed
chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.80_20_quantiles_normalized.genebody.bed
chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.80_20_quantiles_normalized.promoter.bed
chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.genebody.bed
chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.promoter.bed

data_processing:
Raw ChIP-seq reads were mapped using STAR with the following options --alignIntronMax 5 --outFilterMismatchNmax 10 --outFilterMultimapNmax 1  --alignEndsType EndToEnd. Only samples with >1mln unique non-duplicated reads were used for the analysis.
Aligned BAM files from each ChIP-sample were then normalized by the corresponding input samples using bamCompare from deeptools  with the following options: --operation log2 --ignoreDuplicates --effectiveGenomeSize 119481543 and bigwig and bedgraph files were created.
Read coverage over loci and promoters was estimated using bedtools map on the bedgraph files with the “mean” operation.
To estimate the variation of the histone modification levels, the chip-seq coverage values were normalized again to achieve the same range of values across accessions. For this we applied a quantile normalization, setting the 20%- and 80%-quantile values for each sample to the same value with the function in R: quantile_minmax <- function(x) {(x-quantile(x,.20)) / (quantile(x,.80) - quantile(x,.20))}.
the processed data files contain  input-normalized (or input and quantile normalized)  ChIP-seq coverage values averaged across replicates for each accession/histone mark. Most accessions/marks had 2 replicates, but some are completely missing and some only have 1 replicate because we did not manage to get enough unique-non-duplicated reads (>1mln) in those data samples, or there was another quality problem with the data samples such as potential contamination: such samples were exculded, were not used for the analyses and are not submitted as part of this dataset.
Assembly: TAIR10
Supplementary files format and content: chip.5marks.14accessions.Araport11_PCs_TEs.log2_input_normalized_coverage.80_20_quantiles_normalized.genebody.bed is a table with ChIP seq coverage for up to 5 histone marks in 14 accessions, input normalized calculated over the whole locus and quantile normalized. Araport PC genes and TEs. replicates were averaged for each accession/antibody
Supplementary files format and content: chip.5marks.14accessions.Araport11_PCs_TEs.log2_input_normalized_coverage.genebody.bed  is a table with ChIP seq coverage for up to 5 histone marks in 14 accessions, input normalized calculated over the whole locus. Araport PC genes and TEs.
Supplementary files format and content: chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.80_20_quantiles_normalized.genebody.bed  is a table with ChIP seq coveragefor up to 5 histone marks in 14 accessions, input normalized calculated over the whole locus and quantile normalized. Annotation of 5 gene types produced in this study
Supplementary files format and content: chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.80_20_quantiles_normalized.promoter.bed  is a table with ChIP seq coverage for up to 5 histone marks in 14 accessions, input normalized calculated overpromoters (TSS+/-200bp)and quantile normalized. Annotation of 5 gene types produced in this study
Supplementary files format and content: chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.genebody.bed  is a table with ChIP seq coverage for up to 5 histone marks in 14 accessions, input normalized calculated over the whole locus. Annotation of 5 gene types produced in this study
Supplementary files format and content: chip.5marks.14accessions.ourannotation.log2_input_normalized_coverage.promoter.bed  is a table with ChIP seq coverage for up to 5 histone marks in 14 accessions, input normalized, calculated over promoters (TSS+/- 200bp). Annotation of 5 gene types produced in this study

organism: Arabidopsis thaliana

source_name: leaves (developmental stage: 14-leaf-rosette)

growth_protocol: 21 degrees Celcius, on soil, long-day conditions (16h light, 8h dark)

extract_protocol:
DNA isolation using Qiagen PCR purification kit Qiaquick with 0.3M Sodium Acetate
ChIP-seq libraries were prepared from a half of the resulting DNA sample (due to very low amounts we did not measure the DNA concentrations) with the NEBNext Ultra II DNA kit (New England Biolabs) according to the manufacturer’s protocol

tag: treatment

value: INPUT


title: Donor 3 (64), experience 2 (26), Treg, TS-CAR (HA)

source_name: Peripheral blood naive Treg

value: Tregs


title: 5d_CV zebrafish rep3


title: 9905.rep2.H1


title: 9905.rep1.INPUT


title: 9905.rep1.H3K9me2


title: 9905.rep2.H3K4me3


title: 9905.rep1.H3K36me3


title: 9905.rep2.H3K9me2


title: 9905.rep1.H3K4me3


title: Donor 3 (64), experience 2 (26), Treg, non-TS CAR (CD19)


title: Donor 2 (55), experience 1 (24), CD4s, TS-CAR (HA)


title: Donor 2 (55), experience 1 (24), CD4s, non-TS CAR (CD19)


title: 9905.rep1.H3K27me3


title: Donor 3 (64), experience 2 (26), Treg, untransduced


title: Donor 2 (55), experience 1 (24), CD4s, untransduced


title: Donor 1 (52), experience 1 (24), CD4s, non-TS CAR (CD19)


title: 9905.rep1.H1


title: Donor 2 (55), experience 1 (24), Treg, TS-CAR (HA)


title: 9888.rep2.INPUT


title: 9888.rep2.H3K36me3


title: 9905.rep2.H3K36me3


title: Donor 2 (55), experience 1 (24), Treg, untransduced


title: Donor 1 (52), experience 1 (24), Treg, TS-CAR (HA)


title: 9888.rep1.INPUT


title: Donor 1 (52), experience 1 (24), CD4s, TS-CAR (HA)


title: Donor 1 (52), experience 1 (24), Treg, non-TS CAR (CD19)


title: 9888.rep1.H1


title: KARPAS_D14Crizo100nm_B

first: Roberto

last: Chiarle

state: Massachusetts

address: 300 Longwood Avenue

department: Department of Pathology

institute: Children’s Hospital Boston and Harvard Medical School

data_processing:
The designed sgRNA sequences in GeCKO library were aligned to FASTQ file of each sample by using BLAST aligner, allowing maximum 2 bases mismatch. The number of uniquely exactly matched or aligned reads for each sgRNA was counted. The reads count for each unique sgRNA for a given sample were normalized to RPM (Reads Per Million mapped reads) to represent gRNA value. Then we used the MAGeCK algorithm to identify enrichment genes rank by comparing crizotinib treatment over DMSO based on sgRNAs counts, as well as depletion genes rank by DMSO over day 0.
Supplementary_files_format_and_content: txt file for sgRNA reads count and normalized RPM

source_name: ALK+ ALCL cell line

growth_protocol: TS, SU-DHL1, COST and KARPA299 cells are cultured in RPMI containing 10% FBS, P/S, and glutamine (typically 2–3 × 106 cells into a T75 flask).

extract_protocol:
Genomic DNA was extracted using Phenol/Chloroform protocol.
Two round of PCR reaction was used for library constrution. For the first PCR, primers that amplify the lentiCRISPR sgRNA were used for 18 cycles and for each sample, 13 separate 100ul reactions with 10ug genomic DNA was used. The amplicons were combined and second round PCR was performed to attach Illumina adaptors for 18 cycles. The reaction was performed with 5ul of first PCR in 100ul reaction volume. The resulting amplicons were gel extracted and quantified and mixed and sequenced using one end - pairing  Illumina Next Generation Sequencing following the manufacturer's protocols.
Next Generation 500 Illumina Sequencing

treatment_protocol: TS and SU-DHL1 cells were treated with crizotinib every 48hrs. COST and KARPAS299 cells were treated with crizotinib every 24hrs.

tag: cell line

value: 100nM Crizotinib

value: Lymphoma


title: 9888.rep1.H3K9me2


title: 9518.rep1.INPUT


title: 9888.rep1.H3K27me3


title: Donor 1 (52), experience 1 (24), Treg, untransduced

tag: donor


title: KARPAS_D14DMSO_B

value: DMSO

tag: cell type


title: 9888.rep1.H3K36me3


title: 9888.rep1.H3K4me3


title: KARPAS_D0_A


title: KARPAS_D14Crizo100nm_A


title: 9518.rep1.H3K4me3


title: 9888.rep2.H3K9me2


title: KARPAS_D14DMSO_A


title: KARPAS_D0_B


title: Donor 2 (55), experience 1 (24), Treg, non-TS CAR (CD19)


title: COST_D14Crizo50nm_A

value: COST

value: 50nM Crizotinib


title: 9518.rep1.H3K36me3


title: COST_D14Crizo50nm_B


title: 9888.rep2.H1


title: 9518.rep1.H1


title: COST_D14DMSO_B


title: 9057.rep2.INPUT


title: COST_D14DMSO_A


title: 9057.rep2.H3K9me2


title: COST_D0_B


title: 9057.rep2.H3K4me3


title: 9518.rep1.H3K9me2


title: COST_D0_A


title: SUDHL1_D14Crizo80nm_rep2_B

value: 80nM Crizotinib


title: 9057.rep2.H3K36me3


title: SUDHL1_D14Crizo80nm_rep1_B


title: SUDHL1_D14Crizo80nm_rep2_A


title: SUDHL1_D0_rep2_B


title: 9057.rep1.INPUT


title: 9057.rep2.H1


title: SUDHL1_D14DMSO_A


title: 9057.rep1.H3K9me2


title: 9057.rep1.H3K27me3


title: 9057.rep1.H3K4me3


title: 9057.rep1.H1


title: SUDHL1_D14DMSO_B


title: SUDHL1_D0_rep2_A


title: 6966.rep2.INPUT


title: SUDHL1_D0_rep1_A


title: 6966.rep2.H3K9me2


title: 6966.rep2.H3K4me3


title: 9057.rep2.H3K27me3


title: SUDHL1_D0_rep1_B


title: 6966.rep2.H3K36me3


title: TS_D14Crizo80nm_rep2_A

value: TS


title: TS_D14Crizo80nm_rep2_B


title: 9905.rep2.H3K27me3


title: 6966.rep2.H3K27me3


title: TS_D14Crizo80nm_rep1_B


title: SUDHL1_D14Crizo80nm_rep1_A


title: 6966.rep2.H1


title: TS_D14Crizo80nm_rep1_A


title: TS_D14DMSO_rep2_B


title: 6966.rep1.INPUT


title: 6966.rep1.H3K9me2


title: TS_D14DMSO_rep1_B


title: TS_D14DMSO_rep2_A


title: 6966.rep1.H3K4me3


title: 6911.rep1.INPUT


title: TS_D0_rep2_B


title: TS_D0_rep1_B


title: TS_D14DMSO_rep1_A


title: 6911.rep1.H3K4me3


title: TS_D0_rep2_A


title: 6966.rep1.H3K27me3


title: 6911.rep1.H3K36me3


title: 6966.rep1.H1


title: 6911.rep1.H1


title: 6966.rep1.H3K36me3


title: TS_D0_rep1_A


title: 6909.rep2.INPUT


title: S.9905.rep1

description:
150bp PE
TPMs.4_tissues.our_annotation.bed
TPMs.4_tissues.Araport11_annotation.bed

data_processing:
raw RNA-seq reads were aligned to the TAIR10 genome using STAR (v.2.7.1.). First the genomebuild was performed for TAIR10 accounting for the genome size and not providing the annotated splice junctions. The genomebuild command: STAR --runMode genomeGenerate  --genomeSAindexNbases 12.5 --genomeDir $stargenomedir --genomeFastaFiles genome.fasta . The command used for alignment:  STAR --readFilesIn  $fastq.gz  --readFilesCommand zcat --runThreadN 4 --alignIntronMax 6000 --alignMatesGapMax 6000 --genomeDir $stargenomedir --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNoverReadLmax 0.1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMultimapNmax 10 --outReadsUnmapped None --alignSJoverhangMin 8 --outSAMattributes NH HI AS nM NM MD jM jI XS --outSAMtype BAM SortedByCoordinate  --runMode alignReads --twopassMode Basic --outFileNamePrefix $out
read counts were calculated using featurecounts from the subread package (v.2.0.0). Command used: featureCounts  -T 4 -p  -F SAF -O -s 2  -t exon -g gene_id -a $saf -o $out.txt $bam
TPMs were calculated by dividing the raw counts number by the total number of raw counts in the sample (in million reads) and the length (in kb). Command used  sum=`cat $out.txt| awk -v OFS="\t" '{ sum += $7} END {print sum}'`  cat $out.txt| grep -v Geneid| awk -v OFS="\t" -v sum="$sum" ' {print $1,$6,$7,$7*1000000*1000/($6*sum)}' > $out.counts_tpm.bed
Assembly: TAIR10
Supplementary files format and content: TPMs.4_tissues.our_annotation.bed contains a table with TPMs for 5 gene types in the new annotation (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every RNAseq sample
Supplementary files format and content: TPMs.4_tissues.Araport11_annotation.bed contains a table with TPMs for Araport11 annotated genes and TEs for every RNAseq sample

source_name: 7-day-old seedlings with roots

growth_protocol: 22 degrees Celcius, on soil, long-day conditions (16h light, 8h dark)

extract_protocol:
RNA was isolated and DNAse I (NEB) treated using a KingFisher Robot with an in-house magnetic RNA isolation kit. RNA was diluted in nuclease free water (Ambion) and stored at -80oC.
TruSeq Stranded mRNA

value: 7-day-old seedlings with roots


title: S.9764.rep1


title: S.9888.rep1


title: S.9981.rep1


title: S.9728.rep1


title: 6909.rep2.H3K4me3


title: 6909.rep2.H3K9me2


title: S.9638.rep1


title: 6909.rep2.H3K36me3


title: 6909.rep1.INPUT


title: 6909.rep2.H1


title: S.8236.rep1


title: S.9075.rep1


title: S.6966.rep1


title: S.9543.rep1


title: S.6909.rep1


title: 6909.rep1.H3K9me2


title: S.6069.rep1


title: S.6244.rep1


title: 6024.rep2.INPUT


title: 6909.rep1.H3K36me3


title: 6909.rep1.H3K27me3


title: 6909.rep1.H1


title: 6909.rep1.H3K4me3


title: S.22006.rep1


title: 6024.rep2.H3K27me3


title: 6024.rep2.H3K36me3


title: 6024.rep2.H1


title: 6024.rep1.INPUT


title: 6909.rep2.H3K27me3


title: S.6024.rep1


title: S.22004.rep1


title: S.9537.rep1


title: 6024.rep1.H3K9me2


title: S.22005.rep1


title: S.22003.rep1


title: S.6124.rep1


title: S.22002.rep1


title: 6024.rep2.H3K9me2


title: 6024.rep1.H3K36me3


title: S.22001.rep1


title: 6024.rep1.H3K4me3


title: S.1741.rep1


title: C0_4, control_RNAi, 0_hr, biol_rep_4

city: Oklahoma

first: David

middle: J

last: Forsthoefel

state: OK

address: 825 NE 13th St

department: Genes and Human Disease Research Program

institute: Oklahoma Medical Research Foundation

data_processing:
Read quality was assessed with FastQC (v0.11.5) before and after trimming with BBDuk (v36.99) for paired end reads: k=13 ktrim=r mink=11 qtrim=rl trimq=10 minlength=35 tbo tpe.
Reads were mapped to the dd_Smed_v6 transcriptome restricted to 28,069 unique transcripts as in (Forsthoefel et al., eLife, 2020) using Bowtie2 (v2.3.1) for paired end reads, with "-a" multi-mapping and "--local" soft-clipping allowed.
Read summarization was conducted with the "featureCounts" utility in the Subread package (v1.6.3) (Liao et al., Nuc. Acids Res., 2019), using a custom ".SAF" file and options "-p -M -O -F SAF" to include multi-mapping and multi-overlapping reads.
Assembly: Dresden S. mediterranea transcriptome dd_Smed_v6 (http://planmine.mpi-cbg.de/) (Brandl et al., Nuc. Acids Res., 2016)
Supplementary files format and content: Processed data are in a tab-delimited .txt file, wich includes geneID, transcript length, log2 Fold Changes, logCPM,and FDR-adjusted P value.

organism: Schmidtea mediterranea

source_name: anterior third of tail fragments

growth_protocol: Asexual Schmidtea mediterranea (clonal line CIW4) were maintained in Montjuic water and fed with beef liver paste. Planarians were starved 5-7 days prior to initiation of RNAi experiments.

extract_protocol:
Total RNA was extracted from the anterior third of 10 planarian tail fragments per biological replicate using Trizol as described (Forsthoefel et al., eLife, 2020).
Total RNA for 4 biological replicates per condition was submitted to GENEWIZ (South Plainfield, NJ) for library generation from ~ 500 ng/sample using the NEB NEXT ULTRA Library Prep Kit and RNA sequencing with standard Illumina adapters.

treatment_protocol: Planarians were fed twice per week (6 feedings total) with 2 µg dsRNA mixed with 1 µl blue food coloring, 8 µl water, and 40 µl 2:1 liver:water homogenate, then starved seven days prior to amputation.

tag: strain/biotype

value: clonal line CIW4

value: anterior third of tail fragments

value: 0 hours post-amputation


title: E0_1, egr-2_RNAi, 0_hr, biol_rep_1

tag: genotype


title: 6024.rep1.H1


title: C0_3, control_RNAi, 0_hr, biol_rep_3


title: C0_1, control_RNAi, 0_hr, biol_rep_1


title: S.10024.rep1


title: C0_2, control_RNAi, 0_hr, biol_rep_2


title: 6021.rep2.INPUT


title: 6021.rep2.H3K9me2


title: S.10015.rep1


title: E4_3, egr-2_RNAi, 4_dpa, biol_rep_3

value: 4 days post-amputation


title: S.10015.rep2


title: E4_1, egr-2_RNAi, 4_dpa, biol_rep_1


title: E4_4, egr-2_RNAi, 4_dpa, biol_rep_4


title: E4_2, egr-2_RNAi, 4_dpa, biol_rep_2


title: S.10002.rep1


title: C4_3, control_RNAi, 4_dpa, biol_rep_3


title: 6021.rep2.H3K4me3


title: C4_4, control_RNAi, 4_dpa, biol_rep_4


title: 6024.rep1.H3K27me3


title: S.22007.rep1


title: C4_2, control_RNAi, 4_dpa, biol_rep_2


title: R.9981.rep1

source_name: 9-leaf rosette (full rosette)

value: 9-leaf rosette (full rosette)


title: 6021.rep2.H3K27me3


title: 6021.rep2.H1


title: E2_4, egr-2_RNAi, 2_dpa, biol_rep_4

value: 2 days post-amputation


title: R.9888.rep1


title: 5856.rep2.INPUT


title: E2_1, egr-2_RNAi, 2_dpa, biol_rep_1


title: C4_1, control_RNAi, 4_dpa, biol_rep_1


title: E2_2, egr-2_RNAi, 2_dpa, biol_rep_2


title: C2_3, control_RNAi, 2_dpa, biol_rep_3


title: R.9905.rep1


title: C2_4, control_RNAi, 2_dpa, biol_rep_4


title: R.9764.rep1


title: R.9728.rep1


title: R.9638.rep1


title: E0_3, egr-2_RNAi, 0_hr, biol_rep_3


title: C2_1, control_RNAi, 2_dpa, biol_rep_1


title: E0_4, egr-2_RNAi, 0_hr, biol_rep_4


title: 5856.rep2.H3K36me3


title: R.9543.rep1


title: 6021.rep2.H3K36me3


title: E0_2, egr-2_RNAi, 0_hr, biol_rep_2


title: Chlamydomonas reinhardtii, Gamma-ray, 50Gy

city: Jeongeup-si

first: Jin-Hong

last: Kim

state: Jeonbuk-do

address: 29 Geumgu-gil

country: South Korea

institute: Korea Atomic Energy Research Institute

data_processing:
The quality of FASTQ was evaluated using FastQC v0.11.5
dirty' reads were removed using the Trimmomatic v0.36
clean' reads were mapped to NCBI Chlamydomonas reinhardtii v5.5 reference genome using HISAT2 v2.2.1
the number of reads matching each gene in the Chlamydomonas reinhardtii genome was counted using HTSeq-count v0.11.3
Differentially expressed genes (DEGs) were identified from count per million (CPM) normalized read-counts using EdgeR software.
Assembly: Chlamydomonas reinhardtii v5.5 (NCBI)
Supplementary files format and content: tab-delimited text files include read counts for each Sample

organism: Chlamydomonas reinhardtii

source_name: unicellular eukaryote

growth_protocol: 1.5 x 106 cells were cultured in 50 mL TAP media in 250 mL flasks by shaking at 25 oC and 140 rpm under constant white light of 90–100 μmol photons m-2 s-1.

extract_protocol:
1 x 108 of cultured cells were harvested and RNA were extracted using TRIzol reagent.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Plant Kit following manufacturer's protocol.

treatment_protocol: Mid-exponential phase cells of 0.6 OD750 were harvested and subjected to X-irradiation of 6 Gy for 22.2 min at 160 kV and 1 mA, or 50 Gy for 8.1 min at 160 kV and 10 mA using a cabinet type X-ray machine (CP-160, Faxitron X-ray LLC, Lincolnshire, IL, USA). Alternatively, they were also exposed to gamma-rays of 6 or 50 Gy for 1 h, which were generated from a 3 kCi 60Co source at the Advanced Radiation Technology Institute (Jeollabuk-do, Korea).

tag: strain

value: unicellular eukaryote

value: WT

value: Gamma-ray

tag: dose


title: Chlamydomonas reinhardtii, Gamma-ray, 6Gy


title: R.9537.rep1


title: 5856.rep2.H3K27me3


title: E2_3, egr-2_RNAi, 2_dpa, biol_rep_3


title: Donor 1 (52), experience 1 (24), CD4s, untransduced

value: conventional CD4s

value: untransduced


title: R.9075.rep1


title: Chlamydomonas reinhardtii, X-ray, 50Gy

value: X-ray


title: 5856.rep2.H3K9me2


title: Chlamydomonas reinhardtii, X-ray, 6Gy


title: R.8236.rep1


title: 5856.rep1.INPUT

value: INPUT


title: 5856.rep1.H3K4me3


title: Chlamydomonas reinhardtii, mock

value: mock


title: R.6966.rep1


title: R.6909.rep1


title: A549_siYAP/TAZ#2_rep4

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Assembly: GRCh38.p13
Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.

source_name: A549 cells

growth_protocol: Cells were cultured in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA was isolated 24 hours after transfection using the NucleoSpin RNA II kit (Macherey Nagel, Macherey-Nagel). Only samples with an RNA integrity number (RIN) > 7 were considered for RNA sequencing.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols


title: 5856.rep1.H1


title: A549_siYAP/TAZ#1_rep4


title: R.6244.rep1


title: A549_siCo_rep4

value: NTC


title: 5856.rep2.H1


title: fetal_liver18_rep3

first: Yiqing

last: Zhu

address: No.800 Xiangyin

institute: Naval Medical University

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v3.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: liver tissue

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

value: liver

tag: developmental stage

value: fetal


title: R.6124.rep1


title: 5784.rep2.INPUT


title: A549_siYAP/TAZ#2_rep3


title: 5784.rep2.H3K9me2


title: T47D_withE2_RARA_rep3

city: Boston

data_processing:
HTGTS junction reads for each sample were recognized by designed barcode, primer and bait portion  as previously described (Mara Compagno et al., Nature 2017). The barcode, primer and bait portion of the remained sequences were masked for alignment analysis to determine translocation junctions. Briefly, we aligned sequences to the human genome using BLAT, and then filtered artificial junctions by removing PCR repeats (reads with same junction position in alignment to the reference genome and a start position in the read less than 3 bp apart), invalid alignments (including alignment scores < 30, reads with multiple alignments having a score difference < 4 and alignments having 10-nucleotide gaps) and ligation artifacts (for example, random HaeIII restriction sites ligated to bait breaksite). Translocation junction position was determined based on the genomic position of the 5’ end of the aligned read.
Assembly: hg19
Supplementary files format and content: BED files contain all obtained translocation junctions information including chromosome,corrdinate,read name,align score and strand.

growth_protocol:
RPMI 1640 + 2mM Glutamine + 10% Fetal Bovine Serum (FBS)
MCF7 and T47D cells are grown in RPMI supplemented with 2 mM Glutamine and 10% FBS.

extract_protocol:
Rapid lysis buffer + 10ug/ml Proteinase K, at 56°C, overnight
See Supplemental Experimental procedures from Chiarle et al.  Cell 2011, paragraph Generation of HTGTS libraries by adapter-PCR
Gennomic DNAs were extracte with Rapid lysis buffer containing 20 ug/ml of proteinase K overnight at 56°C.
Library was prepaired with the HTGTS methods previously described (Chiarle at al., Cell, 2011_PMID:21962511; Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells)
We induced DNA DSBs in intron 10 of SHANK2 or in intron 1 of RARA. We used linker forward primer and specific target reverse primers to capture functional fusions.

treatment_protocol:
1 uM beta-estradiol, every 24 hours
Cells were treated with either 0.01% ethanol or 1 uM beta-estradiol every 24 hours for 4days.

value: Estrogen receptor-positive breast cancer

value: 1 uM beta-estradiol


title: adult_liver2_rep2

value: adult


title: adult_liver3_rep3


title: fetal_liver16_rep2


title: fetal_liver12_rep1


title: R.6069.rep1


title: R.6024.rep1


title: 5856.rep1.H3K36me3


title: A549_siYAP/TAZ#1_rep3


title: adult_liver1_rep1


title: T47D_withE2_RARA_rep1


title: 5784.rep2.H3K36me3


title: T47D_withoutE2_RARA_rep3

treatment_protocol:
0.01% Ethanol, every 24 hours
Cells were treated with either 0.01% ethanol or 1 uM beta-estradiol every 24 hours for 4days.

value: 0.01% Ethanol


title: A549_siCo_rep3


title: 5784.rep2.H3K27me3


title: R.22006.rep1

value: 9-leaf rosette (full rosette)


title: A549_siYAP/TAZ#2_rep2


title: R.22007.rep1


title: T47D_withoutE2_RARA_rep2


title: 5784.rep2.H1


title: A549_siYAP/TAZ#1_rep2


title: 5784.rep1.INPUT


title: C2_2, control_RNAi, 2_dpa, biol_rep_2

value: clonal line CIW4

value: anterior third of tail fragments

value: 2 days post-amputation


title: T47D_withE2_RARA_rep2


title: A549_siCo_rep2


title: R.22004.rep1


title: R.22005.rep1


title: 5784.rep1.H3K9me2


title: R.22003.rep1


title: MCF7_withE2_RARA_rep2


title: MCF7_withE2_RARA_rep3


title: 5784.rep1.H3K36me3


title: MCF7_withE2_RARA_rep1


title: R.22001.rep1


title: 5784.rep1.H3K27me3


title: R.1741.rep1


title: R.22002.rep1


title: HLF_siCo_rep4

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Assembly: hg19
Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.

source_name: HLF cells

value: HLF cells

value: Nonsense


title: 5784.rep1.H1


title: HLF_siCo_rep3


title: T47D_withoutE2_RARA_rep1


title: 5856.rep2.H3K4me3


title: A549_siYAP/TAZ#2_rep1


title: 1741.rep2.INPUT


title: MCF7_withoutE2_RARA_rep1


title: 5784.rep2.H3K4me3


title: R.10024.rep1


title: R.10015.rep2


title: 1741.rep2.H3K9me2


title: R.10015.rep1


title: A549_siYAP/TAZ#1_rep1


title: 5784.rep1.H3K4me3


title: T47D_withE2_SHANK2_rep2


title: HLF_siYAP/TAZ#1_rep4


title: MCF7_withoutE2_RARA_rep3


title: A549_siCo_rep1


title: R.10002.rep1


title: MCF7_withoutE2_RARA_rep2


title: T47D_withE2_SHANK2_rep1


title: 1741.rep2.H3K36me3


title: T47D_withoutE2_SHANK2_rep3


title: HLF_siYAP/TAZ#1_rep2


title: HLF_siYAP/TAZ#1_rep3


title: 1741.rep2.H3K27me3


title: P.9905.rep1.batchCT

source_name: pollen

value: pollen


title: P.9981.rep1.batch2


title: 1741.rep2.H1


title: T47D_withoutE2_SHANK2_rep2


title: T47D_withE2_SHANK2_rep3


title: HLF_siCo_rep1


title: HLF_siYAP/TAZ#2_rep4


title: 1741.rep1.INPUT


title: P.9888.rep1.batchCT


title: P.9764.rep2.batch2


title: T47D_withoutE2_SHANK2_rep1


title: MCF7_withE2_SHANK2_rep3


title: P.9764.rep1.batchCT


title: HLF_siYAP/TAZ#2_rep3


title: MCF7_withE2_SHANK2_rep2


title: 1741.rep2.H3K4me3


title: 1741.rep1.H3K9me2


title: HLF_siCo_rep2


title: HLF_siYAP/TAZ#2_rep2


title: P.9728.rep1.batchCT


title: 1741.rep1.H3K36me3


title: MCF7_withE2_SHANK2_rep1


title: HLF_siYAP/TAZ#2_rep1


title: HLF_siYAP/TAZ#1_rep1


title: P.9543.rep1.batchCT


title: MCF7_withoutE2_SHANK2_rep2


title: 1741.rep1.H3K27me3


title: 1741.rep1.H1


title: MCF7_withoutE2_SHANK2_rep3


title: CM_1

city: Guangzhou

first: liu

last: xincheng

address: zhongshan Road 74 Street

institute: sysu

data_processing:
We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC:RNA concentration, RIN value,28S/18S and the fragment length distribution.
We use internal software SOAPnuke to filter reads
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
We mapped clean reads to reference using Bowtie2 and then calculate gene expression  level with RSEM
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: The cells were cultured according to the guideline of ATCC

extract_protocol:
Total RNA was isolated from cultured cell lines. Beads containing oligo (dT) were used to isolate poly(A) mRNA from total RNA. Purified mRNA was then fragmented in fragmentation buffer. Using these short fragments as templates, random hexamer-primers ere used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Short double-stranded cDNA fragments were purified with a QIAquick PCR extraction kit (vendor) and eluted with EB buffer for end repair and the addition of an ‘A’ base. Next, the short fragments were ligated to Illumina sequencing adaptors. DNA fragments of a selected size were gel-purified and amplified by PCR. The amplified library was sequenced using Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: U87 cells were treated with bulk control/0.5mM 8-cpt-cAMP/1nM MS275 or a combination for 48 hours. Total RNA was extracted from 1×10^6 cells with TRIzol Reagent (Thermo Fisher Scientific) and was sent for RNA sequencing

value: 0.5mM 8-cpt-cAMP and 1nM MS275


title: CM_2


title: P.9537.rep1.batch2


title: CM_3


title: M_3

value: 1nM MS275


title: P.9075.rep1.batchCT


title: MCF7_withoutE2_SHANK2_rep1


title: 1254.rep2.INPUT

value: INPUT


title: 1254.rep2.H3K9me2


title: P.6966.rep1.batch2


title: P.8236.rep1.batch2


title: M_2


title: 1741.rep1.H3K4me3


title: M_1


title: 1254.rep2.H3K36me3


title: 1254.rep2.H3K4me3


title: P.9638.rep1.batchCT


title: 1254.rep2.H3K27me3


title: C_3

value: 0.5mM 8-cpt-cAMP


title: P.6244.rep1.batchCT


title: 1254.rep2.H1


title: C_2


title: P.6024.rep1.batchCT


title: 1254.rep1.INPUT


title: Ishikawa H3K27ac HiChIP_E2_rep1

first: Jason

last: Gertz

address: 1950 Cir of Hope Dr

institute: University of Utah

description: HiChIP

data_processing:
Reads were aligned to human hg19 reference genome using HiC-Pro
Hichipper was used to perform restriction site bias-aware modeling of the output from HiC-Pro and to call interaction loops.
In Ishikawa cells, DMSO and E2 treated HiChIP loops were combined to identify all possible putative enhancers and in LNCaP cells, loops from separate replicates were combined.
Loops with less than 3 counts were removed
Assembly: hg19
Supplementary files format and content: bedpe files
Library strategy: HiChIP

source_name: Ishikawa

growth_protocol: T-47D and Ishikawa cells were cultured in RPMI 1640 medium (Gibco) with 10% fetal bovine serum (Gibco) and 1% penicillin–streptomycin (Gibco). LNCaP cells were cultured in RPMI media with 10% FBS supplemented. Cells were incubated at 37°C with 5% CO2.

extract_protocol:
Cells were pelleted, then resuspended and fixed in 1% formaldehyde for 10 minutes. Cells were then treated with 125 mM glycine for 5 minutes to stop crosslinking.
HiChIP and library construction was performed as described in Mumbach et al. Nature Methods 2016 (see supplementary protocol) with the following modifications: Ishikawa cells were digested with restriction enzyme DpnII. Crosslinked chromatin from Ishikawa cells was sonicated using an EpiShear probe-in sonicator (Active Motif) with three cycles of 30 seconds at an amplitude of 40% with 30 seconds rest between cycles. Crosslinked chromatin from T-47D and LNCaP cells was sonicated using Covaris E220 with the settings of fill level=10, duty cycle=5, PIP=140, cycles per burst=200, time=4 mins.

value: Ishikawa

value: Endometrial Adenocarcinoma

tag: hichip antibody

value: H3K27ac (Abcam ab4729)

tag: restriction enzyme

value: DpnII (New England Biolabs)

value: 10nM beta-estradiol for 1 hour


title: Ishikawa H3K27ac HiChIP_DMSO_rep2

description: HiChIP

value: DMSO (veh) for 1 hour


title: P.22007.rep2.batch2


title: 1254.rep1.H3K4me3


title: P.22007.rep1.batchCT


title: 1254.rep1.H3K36me3


title: P.6909.rep1.batch2


title: V_2

value: Vehicle


title: V_3


title: P.22006.rep1.batchCT


title: 1254.rep1.H3K27me3


title: T-47D TAF1 E2

data_processing:
ChIP-seq reads were aligned to hg19 using bowtie v1.1.2 with parameters -m 1 –t –best -q -S -l 32 -e 80 -n 2
Peaks were called using macs2 V 2.1.0.20140616 with the following arguments: macs2 callpeak -B --SPMR --pvalue=1e-10 --mfold 15 100.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: RPMI 1640 medium (Gibco) with 10% fetal bovine serum (Gibco) and 1% penicillin–streptomycin (Gibco)

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes at room temperature and then treated with 125 mM Glycine for 5 minutes to stop crosslinking. Crosslinked cells were then washed with cold PBS and scraped to harvest.
ChIP and library construction was performed as described in Reddy et al, Genome Research, 2009.

value: Breast; Ductal Carcinoma

tag: chip antibody

value: TAF II p250/TAF1 (sc-735)

value: 10 nM 17beta-estradiol

tag: time

value: 1 hour


title: P.22005.rep2.batch2

tag: tissue


title: T-47D TAF1 DMSO

value: DMSO (veh)


title: P.22005.rep1.batchCT

value: pollen


title: 1254.rep1.H1


title: Ishikawa H3K27ac HiChIP_E2_rep2

description: HiChIP


title: V_1


title: P.22003.rep1.batchCT


title: P.22004.rep1.batchCT


title: 10012.rep2.INPUT


title: P.22002.rep1.batch2


title: 10012.rep2.H3K4me3


title: T-47D RARA DMSO


title: 10012.rep2.H3K9me2


title: C_1


title: P.22001.rep1.batch2


title: Ishikawa H3K27ac HiChIP_DMSO_rep1

description: HiChIP


title: T-47D MAX E2


title: 10012.rep1.INPUT


title: T-47D MAX DMSO


title: 10012.rep2.H1


title: P.10024.rep1.batch2


title: E.coli, RTase_MMuLV

city: Wuhan

first: Ziang

address: Wuhan University, No.299, Bayi Road, Wuchang District

institute: Wuhan University

data_processing:
Fastq files were trimmed adapter using Trim Galore (v0.6.7)
Trimmed reads were mapped to E. coli str. K-12 substr. MG1655 rRNA sequence using bowtie2 (v2.2.5) and then unmapped reads were mapped to the whole genome
Clean reads were used to call peaks using MACS2 (options: -q 1e-5, v2.2.6)
high repeatability peaks between biological replicates were get using IDR (options: --rank p.value, v2.0.4.2)
RT-stop rates of all sites in peaks were calculated using custom scriptslated using custom scripts
The rRNA-removed reads were also mapped to 9 tRNA sequence using bowtie2 (v2.2.5) to calculate RT-stop rate using custom scripts.
Assembly: E. coli str. K-12 substr. MG1655
Supplementary files format and content: txt, known site tRNA RT-stop rate result
Supplementary files format and content: BED,IDR result (only two groups)

organism: Escherichia coli K-12

source_name: bacterial cell

growth_protocol: E. coli grown on LB with 0.1% ampicillin at 37oC

extract_protocol:
Total RNA was extracted by using the RNA isolation reagent TRI Reagent® (Sigma-Aldrich) following the manufacturer’s instructions.
Total RNA was fragmented and treated/no-treated with ReACT strategy labeled with azide group. DBCO-s-s-Biotin was used to enrich target sequences. Then library was conducted following the illumina's instruction.
ReACT-seq: a method for the detection of 2-methlythio modification in total RNA

value: bacterial cell

tag: substrain

value: DBCO-s-s-Biotin not used


title: T-47D RARA E2

city: Salt Lake City


title: E.coli, RTase_HIV-RT


title: P.10015.rep2.batch2


title: P.1741.rep1.batchCT


title: T-47D LSD1 DMSO


title: T-47D c-MYC E2

value: c-MYC (sc-40)


title: 10012.rep1.H3K4me3


title: P.10015.rep1.batch2


title: 10012.rep1.H3K9me2


title: P.10002.rep1.batch2


title: 10012.rep2.H3K36me3


title: E.coli, RTase_SS


title: T-47D LSD1 E2


title: 10012.rep1.H3K36me3


title: 10012.rep1.H3K27me3


title: T-47D c-JUN DMSO

value: c-JUN (BD Biosciences 558036)


title: T-47D Input

value: none (input)


title: E.coli, control, rep4


title: T-47D c-JUN E2


title: 10012.rep1.H1


title: E.coli, control, rep3


title: F.9981.rep2.batch2

source_name: flowers and flower buds

value: flowers and flower buds


title: F.9981.rep1.batch1


title: E.coli, control, rep2


title: T-47D H3K4me3 E2

value: H3K4me3 (Cell Signaling 9751S)

value: 8 hour


title: T-47D H3K4me3 DMSO


title: F.9905.rep1.batchCT


title: E.coli, control, rep1


title: F.9888.rep1.batchCT


title: E.coli, treated, rep4

value: DBCO-s-s-Biotin used


title: F.9764.rep2.batch2


title: T-47D H3K4me1 E2

value: H3K4me1 (Cell Signaling 5326S)


title: T-47D H3K4me1 DMSO


title: F.9728.rep1.batchCT


title: E.coli, treated, rep3


title: E.coli, treated, rep2


title: T-47D H3K27me3 DMSO

value: H3K27me3 (Active Motif AB_2561020)


title: E.coli, treated, rep1


title: F.9638.rep1.batchCT


title: F.9764.rep1.batchCT


title: Ishikawa TAF1 E2

value: Ishikawa

value: Endometrial Adenocarcinoma

value: TAF II p250/TAF1 (Santa Cruz sc-735)