title: timeseries sample644

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Library strategy: DNA-Seq
Mutation identification: In each sequence read, the distance between a fixed sequence at the start and at the end are determined and used to calculate a score, defined as the difference between the measured distance in the read and the expected distance in a wild-type sequence. Insertions and deletions have score >0 and <0, respectively. A point mutation has score=0, but some bases in the sgRNA target site differ from the wild-type sequence. The intact type specifies reads identical to wild-type sequences.   Per time point, the ratio of each type over the total of reads is calculated. We observed only 2 - 6.5% sequence reads in which we could not find a match with the constant parts and we discarded these reads in subsequent analyses. The called point mutations (score = 0) showed a very similar kinetic profile as the intact sequence (wild-type), indicating that they are mostly sequencing errors. We therefore assigned them as intact sequence in the analysis. Insertion and deletion levels at time point t = 0 h were considered as background and subtracted from all time points.  In the double-cut assays, paired end sequencing was performed. The forward and reverse read were matched by the unique sequence ID of a pair of reads. The deletion events were divided into two types: (i) perfectly excised DNA, and (ii) excised DNA with an indel when the deletion was larger than the expected excised product or up to 5 nucleotides smaller.
Supplementary_files_format_and_content: txt files with barcode, indel type, indel score, sequence; sum txt files with indel type, indel score of pool

source_name: K562 + DD-Cas9

growth_protocol: We established K562#17, which is a clonal cell line of the female K562 cells (American Type Culture Collection) stably expressing DD-Cas9. K562#17 cells were cultured in RPMI 1640 (Life Technologies) supplemented with 10% fetal bovine serum (FBS, HyClone®), 1% penicillin/streptomycin.

extract_protocol:
Cells were collected by centrifugation (300xg, 5 min) and the genomic DNA was isolated using the Isolate II Genomic DNA Kit (Bioline).
PCR was performed in two steps; PCR1 with ~100 ng genomic DNA and site specific barcoded primers. PCR2 used 2 µL of each PCR1 product with Illumina PCR Index Primers Sequences 1–12. Each sample was generated with a unique combination of a barcode and index. Both PCR reactions were carried out with 25 µL MyTaq Red mix (Bioline), 4 µM of each primer and 50 µL final volume in a 96 well plate. PCR conditions were 1 min at 95 ˚C, followed by 15 sec at 95 ˚C, 15 sec at 58 ˚C and 1 min at 72 ˚C (15x). 20 µL of 8 samples were pooled and 100 µL was loaded onto a 1% agarose gel. PCR product was cut from gel to remove the primer dimers and cleaned with PCR Isolate II PCR and Gel Kit (Bioline).

treatment_protocol: For transient transfection, 6x106 K562 cells were resuspended in self-made transfection buffer (100 mM KH2PO4, 15 mM NaHCO3, 12 mM MgCl2, 8 mM ATP, 2 mM glucose (pH 7.4)) (Hendel et al., 2014). After addition of 3.0 µg plasmid DNA, the cells were electroporated in an Amaxa 2D Nucleofector using program T-016. DD-Cas9 was induced with a final concentration of 500 nM Shield-1 (Aobious).  For kinetics experiments, 18x106 cells were transfected and divided over 12-well plates, one well for each time point and each well carrying 1x106 cells. Cas9 was activated 24h after nucleofection and cells were collected at the indicated time points after Cas9 induction. As controls, cells without Shield-1 were collected at various time points. DNA-PKcs inhibitor NU7441 (Cayman) (final concentration 1 µM) or DMSO (control) was added to K562#17 at the same time when the cells were supplemented with Shield-1 to induce DD-Cas9. 10 Gy of IR was administered by Cs source Gammacell®40 Exactor (Best Theratronics).

value: K562#17 clone with DD-Cas9 stably integrated

tag: sgrna target site

value: sgRNA chr11

tag: time point

tag: time series + conditions

tag: conditions

value: +shield


title: timeseries sample647

status: Public on May 01 2018

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: strain


title: timeseries sample645


title: timeseries sample642

value: sgRNA LBR8


title: timeseries sample640


title: timeseries sample643


title: timeseries sample641

value: -sgRNA

value: -shield


title: timeseries sample639


title: timeseries sample638


title: timeseries sample633

value: sgRNA AAVS1


title: timeseries sample637


title: timeseries sample636


title: timeseries sample646


title: timeseries sample627


title: timeseries sample632


title: timeseries sample631


title: timeseries sample628


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title: timeseries sample634


title: timeseries sample609


title: timeseries sample610


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title: timeseries sample622


title: timeseries sample608


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title: timeseries sample624


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title: timeseries sample563


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title: timeseries sample531


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title: timeseries sample529


title: timeseries sample524


title: timeseries sample526


title: timeseries sample525


title: timeseries sample546


title: timeseries sample521


title: timeseries sample519

value: --shield


title: timeseries sample520


title: timeseries sample535


title: timeseries sample534


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title: timeseries sample518


title: timeseries sample523


title: timeseries sample517


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title: timeseries sample508


title: timeseries sample528


title: timeseries sample506


title: timeseries sample505


title: timeseries sample507


title: timeseries sample504


title: timeseries sample503

value: -+shield


title: timeseries sample502


title: timeseries sample500


title: timeseries sample498


title: timeseries sample497


title: timeseries sample499


title: timeseries sample501


title: timeseries sample492


title: timeseries sample491


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title: timeseries sample510


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title: timeseries sample437


title: timeseries sample446


title: timeseries sample444

value: sgRNA LBR2+LBR8


title: timeseries sample438


title: timeseries sample449


title: timeseries sample441

value: sgRNA LBR2


title: timeseries sample440


title: timeseries sample452


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title: timeseries sample296


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title: timeseries sample292


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title: timeseries sample302


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title: timeseries sample278


title: timeseries sample293


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title: timeseries sample272


title: timeseries sample274


title: timeseries sample273


title: timeseries sample267


title: timeseries sample265


title: timeseries sample264


title: timeseries sample269


title: timeseries sample262

value: sgRNA LBR2+LBR6


title: timeseries sample261

value: sgRNA LBR2+LBR5


title: timeseries sample268


title: timeseries sample263

value: sgRNA LBR2+LBR7


title: timeseries sample266


title: timeseries sample259

value: sgRNA LBR6


title: timeseries sample258

value: sgRNA LBR2+LBR9


title: timeseries sample260

value: sgRNA LBR7


title: timeseries sample257

value: K562#17 clone with DD-Cas9 stably integrated

value: sgRNA LBR5


title: timeseries sample277

value: +shield


title: timeseries sample256

value: sgRNA LBR2 +LBR8


title: timeseries sample254

value: sgRNA LBR8


title: timeseries sample252

value: -sgRNA

value: +shield  + NU7441


title: timeseries sample253


title: timeseries sample255


title: timeseries sample249

value: -shield  + NU7441


title: timeseries sample248

value: +shield + NU7441


title: timeseries sample250


title: timeseries sample246


title: timeseries sample251


title: timeseries sample243


title: timeseries sample244


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title: timeseries sample237


title: timeseries sample234


title: timeseries sample236


title: larvae  irradiated with 15Gy_IR2, biological rep2

type: RNA

city: Beijing

first: Baoquan

last: Zhao

address: Taiping road,27

country: China

institute: Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences

description:
Gene expression data from zebrafish larvae 7 dpf
zebrafish_15Gy-02

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Danio rerio

source_name: zebrafish larva_15 Gy radiation

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

growth_protocol: The embryos were collected and rinsed with standard zebrafish E3 culture medium (5 mM NaCl, 0.33 mM CaCl2, 0.33 mM MgSO4, 0.15 mM KCl, pH 7.2, conductivity range 470–520 μS), and then, incubated at 28.5 ◦C incubator until experimental use.

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

treatment_protocol: Embryos were attained from multiple clutches for each experimental procedure.The proton beam energy was 8 MeV/u, and the dose rate was 7.5 Gy/min.20 embryos were collected as one sample and stored at −80 ◦C to perform subsequent experiment of RNA extraction and mRNA transcription analysis.

value: AB

tag: development stage

value: 7 days post fertalization

tag: tissue

value: lavae

tag: irradiated with

value: 15 Gy radiation


title: timeseries sample235

value: sgRNA LBR2


title: timeseries sample233


title: larvae irradiated with 15Gy_IR2, biological rep1

description:
Gene expression data from zebrafish larvae 7 dpf
zebrafish_15Gy-01


title: larvae unirradiated_CK, biological rep1

description:
Gene expression data from zebrafish larvae 7 dpf
zebrafish_Control-01

source_name: zebrafish larva_0 Gy radiation

value: none (unirradiated)


title: larvae irradiated with 12Gy_IR1, biological rep1

description:
Gene expression data from zebrafish larvae 7 dpf
zebrafish_12Gy-01

source_name: zebrafish larva_12 Gy radiation

value: 12 Gy radiation


title: 21 day old hma2/4 Roots Control Rep 1

city: Bochum

first: Scott

last: Sinclair

address: Universitaetstrasse 150

country: Germany

institute: Ruhr Universitaet Bochum

description: Gene expression data from Arabidopsis

hyb_protocol: Hybridisation was performed according to the manufacturers instructions at Gene Core, EMBL Heidelberg

scan_protocol: Scanning was performed at Gene Core, EMBL Heidelberg

data_processing:
All data were imported into Genespring (Version 8, Agilent Technologies), and a MAS5 summarization/normalization performed. To account for random fluctuations that influence the signal intensity of lowly expressed probes, entities in 25th percentile of signal intensities in all microarray hybridizations were filtered out.
Probe sets were identified that showed a 2-fold or larger average difference between conditions or between genotypes. Probe sets of interest were further narrowed down by selecting only those that showed a 2-fold or larger difference in each of both replicate experiments. These data were then subjected to an unpaired Mann-Whitney test with a cut-off value of P < 0.2.

organism: Arabidopsis thaliana

source_name: Root

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol at Gene Core ,EMBL Heidelberg

growth_protocol: In the case of the wild-type in control vs. Zn-deficiency comparison, wild-type plants were grown in hydroponic conditions for 7 weeks. In the wild-type vs. hma2 hma4 comparison, plants were grown for 21 days on solidified-agar control medium

extract_protocol: Shoot and root tissue was snap-frozen in liquid nitrogen and ground with a mortar and pestle. ~ 500mg of tissue was applied to the QiaShredder column, and RNA extracted using the Qiagen Plant RNAeasy Kit and protocol

treatment_protocol: In the week old control vs. Zn-deficiency experiment, after 4 weeks in control conditions plants transferred to either control or Zn-deficient media for a further 3 weeks. 7 day old wild-type and hma2 hma4 seedlings were transferred from control media to vertical plates containing control media for a further 14 days growth

tag: age

value: 21 day old

tag: condition

value: Control

tag: genotype

value: hma2 hma4

value: Root


title: larvae  irradiated with 15Gy_IR2, biological rep3

description:
Gene expression data from zebrafish larvae 7 dpf
zebrafish_15Gy-03


title: timeseries sample232

value: K562#17 clone with DD-Cas9 stably integrated

value: +shield


title: timeseries sample238


title: 21 day old hma2/4 Shoots Control Rep 2

description: Gene expression data from Arabidopsis

source_name: Shoot

value: Shoot


title: 21 day old WT Roots Control Rep 2

description: Gene expression data from Arabidopsis

value: WT


title: 7 week old WT Roots -Zn Rep 2

description: Gene expression data from Arabidopsis

value: 7 week old

value: -Zn


title: 21 day old WT Shoots Control Rep 2

description: Gene expression data from Arabidopsis


title: 21 day old WT Roots Control Rep 1

description: Gene expression data from Arabidopsis


title: timeseries sample231

value: -shield


title: timeseries sample229


title: timeseries sample230

value: +shield + NU7441


title: 21 day old hma2/4 Roots Control Rep 2

description: Gene expression data from Arabidopsis


title: 7 week old WT Roots -Zn Rep 1

description: Gene expression data from Arabidopsis


title: 7 week old WT Shoots -Zn Rep 1

description: Gene expression data from Arabidopsis


title: timeseries sample228


title: timeseries sample227


title: 7 week old WT Roots Control Rep 1

description: Gene expression data from Arabidopsis


title: 21 day old WT Shoots Control Rep 1

description: Gene expression data from Arabidopsis


title: timeseries sample247


title: timeseries sample225


title: 7 week old WT Shoots Control Rep 2

description: Gene expression data from Arabidopsis


title: timeseries sample223


title: timeseries sample224


title: 7 week old WT Roots Control Rep 2

description: Gene expression data from Arabidopsis


title: timeseries sample226


title: Nerve Root_5w_AN_rep1

city: nantong

first: hongkui

last: wang

address: 19# qixiu road

institute: nantong university

description:
5W AN1
Gene expression after 5w  in spinal nerve root

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 14.1(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Mus musculus

source_name: Nerve Root_5w_AN

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

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

treatment_protocol: The efferent and afferent nerve fibers arising from spinal cord segments L4-L6 were dissected and separately collected into eight tubes containing Lysis/Binding Buffer (Ambion; Austin, TX). Tissues were electronically homogenized on ice and then centrifuged at 13,200 rpm for 15 min at 4°C. The resulting supernatant was collected and used in the following total RNA isolation steps.

tag: developemetal stage

value: L4-L6 segments of the spinal cord

tag: tissue subtype

value: afferent nerve (AN)  fibres


title: Nerve Root_5w_EN_rep2

description:
5W EN2
Gene expression after 5w  in spinal nerve root

source_name: Nerve Root_5w_EN

value: efferent nerve (EN)  fibres


title: 2-week-old seedlings grown on MS plates, 10 µM estradiol treatment, 4h time point

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

description: Gene expression data from estradiol-induced seedlings

hyb_protocol: Staining, hybridisation and washing was carried out on the Affymetrix GeneChip Fluidics Station. The protocol used was the GeneChip Expression Analysis Technical Manual.

scan_protocol: Arrays were scanned on the Affymetrix Scanner and the program software used was GCOS (Gene Chip Operating System).

data_processing: RNA levels measured by Affymetrix ATH1 microarrays and the probe sets were redefined according to Dai et al. (2005). The expression levels of probe sets were then determined by GC robust multi-array (GCRMA) analysis using R package gcrma (Wu et al., 2004).

source_name: Arabidopsis 2-week-old seedlings

label_protocol: Ambion MessageAmpII-96 aRNA Kit.

growth_protocol: Seedlings were grown on MS plates (long-day condition, 16 h light : 8 h dark) for the 3 h and 4 h induction time points; mature leaves were collected from soil-grown plants (12 h : 12 h day : night) for the 6 h induction time point.

extract_protocol: Qiagene RNeasy plant mini kit was used according to the manufacture's instructions.

treatment_protocol: Seedlings and mature leaves were treated with 10 µM estradiol; controls were treated with 0.1% ethanol.

value: Seedlings

value: 2 weeks old

tag: grown on

value: MS plates


title: Deatched mature leaves (from 40-day-old soil-grown plants), 10 µM estradiol treatment, 6h time point

description: Gene expression data from estradiol-induced detached leaves

source_name: Arabidopsis 40-day-old plants, detached leaves

value: Mature leaves

value: 40 days old

value: soil


title: 7 week old WT Shoots -Zn Rep 2

description: Gene expression data from Arabidopsis


title: Deatched mature leaves (from 40-day-old soil-grown plants), control for 6h time point

description: Gene expression data from mock-treated detached leaves


title: Nerve Root_5w_AN_rep3

description:
5W AN3
Gene expression after 5w  in spinal nerve root


title: Nerve Root_3w_EN_rep3

description:
3W EN3
Gene expression after 3w  in spinal nerve root

source_name: Nerve Root_3w_EN


title: 7 week old WT Shoots Control Rep 1

description: Gene expression data from Arabidopsis

value: Control


title: 2-week-old seedlings grown on MS plates, 10 µM estradiol treatment, 3h time point


title: Nerve Root_3w_EN_rep1

description:
3W EN1
Gene expression after 3w  in spinal nerve root


title: Nerve Root_3w_AN_rep3

description:
3W AN3
Gene expression after 3w  in spinal nerve root

source_name: Nerve Root_3w_AN


title: Nerve Root_3w_EN_rep2

description:
3W EN2
Gene expression after 3w  in spinal nerve root


title: Nerve Root_5w_AN_rep2

description:
5W AN2
Gene expression after 5w  in spinal nerve root


title: timeseries sample222

value: K562#17 clone with DD-Cas9 stably integrated

value: sgRNA LBR2


title: Nerve Root_5w_EN_rep3

description:
5W EN3
Gene expression after 5w  in spinal nerve root


title: Nerve Root_5w_EN_rep1

description:
5W EN1
Gene expression after 5w  in spinal nerve root


title: 2-week-old seedlings grown on MS plates, control for 4h time point

description: Gene expression data from mock-treated seedlings


title: Nerve Root_1w_EN_rep3

description:
1W EN3
Gene expression after 1w  in spinal nerve root

source_name: Nerve Root_1w_EN


title: Nerve Root_1w_EN_rep1

description:
1W EN1
Gene expression after 1w  in spinal nerve root


title: Nerve Root_1w_EN_rep2

description:
1W EN2
Gene expression after 1w  in spinal nerve root


title: Nerve Root_3w_AN_rep1

description:
3W AN1
Gene expression after 3w  in spinal nerve root


title: Nerve Root_3w_AN_rep2

description:
3W AN2
Gene expression after 3w  in spinal nerve root


title: Nerve Root_1w_AN_rep3

description:
1W AN3
Gene expression after 1w  in spinal nerve root

source_name: Nerve Root_1w_AN


title: timeseries sample219


title: timeseries sample221


title: 2-week-old seedlings grown on MS plates, control for 3h time point


title: timeseries sample218


title: timeseries sample220

value: +shield


title: Nerve Root_1w_AN_rep2

description:
1W AN2
Gene expression after 1w  in spinal nerve root


title: timeseries sample217


title: timeseries sample216

value: +shield +NU7441


title: timeseries sample215

value: -sgRNA


title: timeseries sample213

value: sgRNA chr11


title: Nerve Root_1w_AN_rep1

description:
1W AN1
Gene expression after 1w  in spinal nerve root


title: timeseries sample214


title: Nerve Root_0h_EN_rep2

description:
P0 EN2
Gene expression after 0h  in spinal nerve root

source_name: Nerve Root_0h_EN


title: Nerve Root_0h_EN_rep3

description:
P0 EN3
Gene expression after 0h  in spinal nerve root


title: Nerve Root_0h_AN_rep3

description:
P0 AN3
Gene expression after 0h  in spinal nerve root

source_name: Nerve Root_0h_AN


title: KO LPS biological rep 2

city: Ann Arbor

first: yaping

last: sun

state: Michigan

address: 1500 E Medical Center Dr.

department: internal medicine

country: USA

institute: university of michigan

description:
Gene expression data from T cells purified ftom 10 weeks old miR-142 KO mouse spleen.
Mouse miR142KO.LPS-2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The stained arrays were scanned on an Agilent Gene Array Scanner (Affymetrix) with a 560-nm filter.

data_processing: The data were calculated as expression values for each gene using a robust multi-array average (RMA). This is a modeling strategy that converts the PM probe values into an expression value for each gene. Note that the expression values are log2 transformed data. Probesets that had a fold change greater than 2 and an adjusted p-value less than .05 were selected.

source_name: DCs from miR-142 KO mouse

label_protocol: Biotinylated cRNA were prepared using the WT-Ovation™ Pico System (Affymetrix), and a single round of amplification for samples with even stricter concentration restraints. This system incorporates oligo(dT) and random primers for amplification at the 3’ end and throughout the whole transcriptome.

growth_protocol: Mice were housed in sterilized microisolator cages and received filtered water and normal chow. All animals were cared for under regulations reviewed and approved by the University Committee on Use and Care of Animals of the University of Michigan, based on University Laboratory Animal Medicine guidelines.

extract_protocol: The tcRNA was extracted from purified WT B6 DCs and miR-142 KO DCs with RNeasy Mini Kit (Qiagen) and the quality of the total RNA was verified by an Agilent 2100 Bioanalyzer.

treatment_protocol: DCs were isolated from individual spleen cells suspensions by positive selection.

tag: stimulation

value: LPS

value: dendritic cells

value: spleen

value: miR-142 KO

tag: background

tag: gender

value: Male


title: KO LPS biological rep 1

description:
Gene expression data from T cells purified ftom 10 weeks old miR-142 KO mouse spleen.
Mouse miR142KO.LPS-1


title: Nerve Root_0h_EN_rep1

description:
P0 EN1
Gene expression after 0h  in spinal nerve root

value: L4-L6 segments of the spinal cord

value: efferent nerve (EN)  fibres


title: KO LPS biological rep 3

description:
Gene expression data from T cells purified ftom 10 weeks old miR-142 KO mouse spleen.
Mouse miR-142KO.LPS3


title: input DNA

city: aarhus

first: Yonglun

last: Luo

address: Wilhelm Meyers Allé 4

country: Denmark

institute: Aarhus University

data_processing:
Reads were aligned to the  human genome (hg19) using the BWA algorithm (default settings). Duplicate reads were removed and only  uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in  silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the sizeselected  library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal  maps”) were stored in bigWig files. For Nrf2, peak locations were determined using the MACS algorithm  (v2.1.0) with a cutoff of p-value = 1e-7. RNA Pol2-enriched regions were identified using the SICER  algorithm at a cutoff of FDR 1E-10 and a max gap parameter of 600 bp. Peaks that were on the ENCODE  blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input  data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed  information on sample comparison, peak metrics, peak locations and gene annotations.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using BWA algorithm using Active Motif software, Since the 5´-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp). To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be visualized in genome browsers (see Section V.). bigWig files also provide the peak metrics in the Active Motif analysis program. An Excel file listing all Intervals (genomic segments where the fragment density is above the threshold) is also included

growth_protocol: Human lung adenocarcinoma epithelial A549 cells are cultured in DMEM (Lonza) supplemented with 10% heat inactivated fetal calf serum, 200 IU.mL-1  penicillin, 100 μg.mL-1 streptomycin and 600 μg.mL-1 glutamine .

extract_protocol:
Lysates were sonicated and the DNA  sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of  chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets  were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to  the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with protein A (for Nrf2) or G (for Pol2) agarose beads  (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of target specific antibody.  Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K  treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenolchloroform  extraction and ethanol precipitation.
Illumina sequencing libraries  were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing,  dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were  quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: A549 cells were fixed with 1%  formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of  lysis buffer, followed by disruption with a Dounce homogenizer.

tag: cell line

value: lung adenocarcinoma

tag: genotype/variation

value: wildtype

tag: chip antibody


title: KO biological rep 3

description:
Gene expression data from T cells purified ftom 10 weeks old miR-142 KO mouse spleen.
Mouse miR-142KO.3

tag: cell type


title: timeseries sample212

source_name: K562 + DD-Cas9

tag: strain

tag: sgrna target site

tag: time point

tag: time series + conditions

tag: conditions

value: -shield


title: siCTRL_Pol2 ChIPSeq

value: Human lung adenocarcinoma epithelial A549 cells

value: siControl

value: RNA Pol II (Active Motif 39097 lot 19)


title: timeseries sample210

value: K562#17 clone with DD-Cas9 stably integrated

value: sgRNA AAVS1

value: +shield


title: timeseries sample211

value: sgRNA chr11


title: KO biological rep 1

description:
Gene expression data from T cells purified ftom 10 weeks old miR-142 KO mouse spleen.
Mouse miR142KO.1

tag: tissue


title: Nerve Root_0h_AN_rep2

description:
P0 AN2
Gene expression after 0h  in spinal nerve root

value: afferent nerve (AN)  fibres


title: WT LPS biological rep 1

description:
Gene expression data from T cells purified ftom 10 weeks old WT mouse spleen.
Mouse B6.LPS-1

source_name: DCs from WT mouse

value: LPS

value: dendritic cells

tag: genotype

value: WT


title: WT LPS biological rep 2

description:
Gene expression data from T cells purified ftom 10 weeks old WT mouse spleen.
Mouse B6.LPS-2

value: spleen

value: Male


title: WT LPS biological rep 3

description:
Gene expression data from T cells purified ftom 10 weeks old WT mouse spleen.
Mouse B6.LPS-3


title: KO biological rep 2

description:
Gene expression data from T cells purified ftom 10 weeks old miR-142 KO mouse spleen.
Mouse miR142KO.2

value: miR-142 KO


title: NRF2_ChIPSeq

value: lung adenocarcinoma

value: anti-NRF2 (Santa Cruz, sc-13032, lot C1416)


title: siNfr2_Pol2ChIPSeq


title: Nerve Root_0h_AN_rep1

description:
P0 AN1
Gene expression after 0h  in spinal nerve root

tag: developemetal stage

value: L4-L6 segments of the spinal cord


title: timeseries sample209

value: -sgRNA


title: timeseries sample208


title: WT biological rep 3

description:
Gene expression data from T cells purified ftom 10 weeks old WT mouse spleen.
Mouse B6.3


title: timeseries sample207

value: sgRNA LBR2

value: +shield +NU7441


title: CDI-2

city: Stanford

first: Marta

last: Diez Cunado

state: Ca

address: 300 pasteur dr rd

institute: Stanford University

description: replicate 2

library_source: transcriptomic

data_processing:
miRBase mature micrRNA version 20 for miRNA annotation
Mapping:  Bowtie2 (Langmead and Salzberg, Nat. Meth. 2012)
Feature summarization:  Expectation-Maximization(EM) approach used to estimate transcript abundance (Jiang and Wong, Bioinformatics, 2009)
Normalization within sample:  RPKM (reads per kilobase of transcript per million, Mortazavi et al, Nat. Meth. 2008)
Criteria for selecting candiate miRNA:At least one sample has read count >= 5
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

source_name: cardiomyocytes

growth_protocol: hiPSC-CMs purchased from Cellular Dynamics (CDI), Inc. were cultured for 14 days in Serum-free medium (SFM): 75% Iscove’s Modified Dulbecco’s Medium (IMDM), 25% Ham’s-F12 medium complemented with 2mM L-Glutamine, 50 U/mL penicillin, 50mg/mL streptomycin, 1% B-27 supplement (GIBCO), 0.5% N-2 supplement (GIBCO), 0.5 mM ascorbic acid, and 0.05% Bovine Serum Albumin (BSA) at 37C in5% CO2 and humidified atmosphere.

extract_protocol:
RNA was extracted using mirVana TM miRNA Isolation Kit (Ambion)
RNA libraries were prepared for sequencing using Truseq smallRNA Illumina protocols

value: CDI

value: Human Induced Pluripotent Stem Cell-derived cardiomyocytes (hiPSC-CMs)


title: timeseries sample206

value: K562#17 clone with DD-Cas9 stably integrated

value: -shield +NU7441


title: CDI-1

description: replicate 1


title: cml39_rep2

city: Kingston

first: Wayne

middle: A

last: Snedden

state: Ontario

address: 116 Barrie St.

department: Biology

country: Canada

institute: Queen's University

data_processing:
Illumina’s CASAVA (v1.8) pipeline was used to generate FASTQ files, and the quality of the reads assessed using FASTQC.
The annotated Arabidopsis gene file (release-33) obtained from ensembl was used to index the TAIR10 genome using STAR aligner v2.5.2b with the following configurations:  --runMode genomeGenerate  --sjdbOverhang 74
Reads were aligned to the indexed genome using STAR aligner v2.5.2b with the following configurations: STAR --quantMode GeneCounts --alignIntronMax 15000 --outFilterMismatchNoverLmax 0.05 --outReadsUnmapped Fastx --outFilterType BySJout
The mapped reads quantified in STAR were used for differential gene expression analysis. Analysis was carried out using DESeq2 v1.14.1.
Genome_build: TAIR10
Supplementary_files_format_and_content: The tab-delimited text file "star_genecounts.txt" contains the number of mapped reads per gene (TAIR10 gene models) as calculated by STAR aligner. The first column contains the gene models. Columns 2-5 contain the number of mapped reads for each respective sample. Abbreviations: wt=wild type samples; cml39=cml39 mutant samples; rep=biological replicate. The tab-delimited text file "deseq2_analysis_cml39_vs_wt.txt" contains a differential gene expression analysis performed in Deseq2. Columns: gene=TAIR10 gene identifiers; baseMean=mean of normalized counts for all samples; log2FoldChange=log2 fold change cml39 vs wt; lfcSE=log fold change standard error; stat=Wald statistic; pvalue=Wald test p-value; padj=BH adjusted p-values.

source_name: seedling

growth_protocol: Plants were grown under 16 h light/8 h dark cycles at 150 µE, 22°C and 70% relative humidity.

extract_protocol:
Total RNA was extracted from 100 mg tissue using the Qiagen RNeasy plant mini RNA extraction kit (Qiagen, http://www.qiagen.com/) according to the manufacturer's instructions.
Strand specific mRNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit.

tag: ecotype

tag: developmental stage

value: 7 day old seedling


title: 21 day old hma2/4 Shoots Control Rep 1

description: Gene expression data from Arabidopsis

tag: age

value: 21 day old

tag: condition

value: Control

value: hma2 hma4

value: Shoot


title: WT biological rep 2

description:
Gene expression data from T cells purified ftom 10 weeks old WT mouse spleen.
Mouse B6.2

tag: stimulation

value: dendritic cells

value: spleen

value: WT

tag: background

tag: gender

value: Male


title: cml39_rep1


title: timeseries sample204

value: sgRNA chr11

value: +shield


title: timeseries sample205

value: sgRNA LBR2


title: wt_rep2


title: wt_rep1


title: WT biological rep 1

description:
Gene expression data from T cells purified ftom 10 weeks old WT mouse spleen.
Mouse B6.1


title: timeseries sample203

value: -shield


title: timeseries sample202


title: timeseries sample201

value: sgRNA AAVS1


title: timeseries sample197


title: timeseries sample198

value: +shield +NU7441


title: timeseries sample199

value: K562#17 clone with DD-Cas9 stably integrated


title: timeseries sample200


title: timeseries sample196


title: timeseries sample195


title: timeseries sample192


title: timeseries sample194


title: timeseries sample193


title: Breast tumor T0247_C

type: genomic

city: Paris

first: Elodie

last: Girard

address: 11-13 rue Pierre et Marie Curie

country: France

institute: Institut Curie

hyb_protocol: Probes annealing and ligation on tumor DNA, amplification by PCR, probes digestion and DNA hybridization on each array were performed according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using fluidics wash, and scanned using the Gene Chip Scanner 3000.

data_processing: Each sample has two CEL files (= array fluorescence intensity files generated per sample by the Affymetrix GeneChip® Command Console (version 4.0, 2013)) , as it was hybridized with two arrays: the A/T array and with the G/C array to obtain the genotype for each SNP present on the OncoScan.  Therefore sample name descriptors _A and _C correspond to the CEL file for the A/T array and for the G/C array, respectively. Copy number values for individual SNPs were extracted and converted from CEL file and processed using the Genome Alteration Print (GAP) method (Popoval et al., Genome Biol, 2009) to determine the ploidy of each tumour and CNV.

label: Biotin

source_name: Breast tumor DNA T0247

label_protocol: Performed according to manufacturer's protocols.

growth_protocol: All samples were formamid-fixed paraffin-embedded tumors.

extract_protocol: Tumor tissues were microdissected from four 10μm section and tumor DNA was extracted from the Macherey-Nagel Nucleospin Tissue protocol according to the manufacturer's instruction. DNA quality and quantity was assessed using Qubit andq-PCR.

treatment_protocol: No treatment was performed

tag: Sex

value: Female

tag: atm status

value: Heterozygote

tag: variant type

value: truncating variant

tag: molecular suptype

value: Luminal B

value: breast tumor


title: Breast tumor T0220_A

source_name: Breast tumor DNA T0220

value: Missense variant


title: Breast tumor T0220_C


title: timeseries sample189

tag: cell type

tag: strain

tag: sgrna target site

tag: time point


title: timeseries sample191

tag: time series + conditions

tag: conditions


title: timeseries sample188

value: -shield +NU7441


title: timeseries sample190


title: Breast tumor T0247_A

tag: tissue


title: timeseries sample187


title: timeseries sample186


title: timeseries sample185


title: Donor 18

city: Barcelona

first: Riccardo

last: Aiese Cigliano

address: Calle Comte D'Urgell 240

country: Spain

institute: Sequentia Biotech SL

hyb_protocol: Bisulfite converted sperm DNA was hybridized onto the 450K methylation array following Illumina Infinium HD Methylation workflow.

scan_protocol: Analysis was performed using the Illumina iScan SQ fluorescent scanner.

data_processing: Raw fluorescence intensities were extracted using GenomeStudio Methylation module software (Illumina, USA).

label: Fluorescent labelled probes on bisulfite converted DNA.

source_name: Ejaculated sperm

label_protocol: Standard Illumina protocol.

extract_protocol: Isolation of spermatozoa genomic DNA was performed with the commercial extraction kit Puregen (Gentra Systems, USA). Samples were centrifuged at 16,000 g for 20 seconds, the supernatant was discarded and the pellet was incubated with the supplied lysis buffer solution supplemented with 1,4- Dithiothreitol 1M and 10 mg/ml Proteinase K. Cell lysis was performed overnight at 55°C with constant vortexing. The protein fraction was extracted by centrifugation at 16,000 g for 3 minutes after a treatment of 5 minutes using the kit-supplied solution. The supernatant was carefully transferred into a fresh microcentrifuge tube containing 300 μl of 100% isopropanol (2-propanol). The sample was centrifuged for 1 minute at 16,000 g, the supernatant discarded and the sample dried at room temperature. Finally, the sample was washed with fresh 70% ethanol, and the pellet recovered and stored at -20ºC in hydration solution.

value: Sperm

tag: fertility status

value: fertile

tag: donor


title: Breast tumor T0176_A

source_name: Breast tumor DNA T0176

value: Luminal B/HER2


title: Breast tumor T0175_C

source_name: Breast tumor DNA T0175

value: Unknown


title: Breast tumor T0175_A


title: timeseries sample183

value: +shield


title: Donor 15

value: Male


title: timeseries sample184

value: sgRNA chr11


title: timeseries sample182

value: sgRNA AAVS1

value: -shield


title: timeseries sample180

value: K562#17 clone with DD-Cas9 stably integrated

value: sgRNA LBR2

value: +shield +NU7441


title: Breast tumor T0174_C

source_name: Breast tumor DNA T0174

value: Heterozygote


title: Donor 17


title: Breast tumor T0174_A


title: Breast tumor T0176_C

value: Female

value: truncating variant


title: timeseries sample179


title: Donor 19


title: Donor 14


title: timeseries sample178


title: Donor 8


title: Donor 11


title: Breast tumor T0120_C

source_name: Breast tumor DNA T0120

value: Missense variant

value: Luminal A

value: breast tumor


title: Breast tumor T0120_A


title: Donor 12

value: Sperm

value: fertile


title: timeseries sample176


title: Donor 13


title: Donor 2


title: timeseries sample174


title: Breast tumor T0123_C

source_name: Breast tumor DNA T0123

value: Luminal B


title: Donor 9


title: Breast tumor T0099_A

source_name: Breast tumor DNA T0099


title: Breast tumor T0123_A


title: Donor 7


title: Breast tumor T0072_C

source_name: Breast tumor DNA T0072

value: Homozygote


title: Donor 4

value: Male


title: timeseries sample171


title: Donor 1


title: Breast tumor T0173_C

source_name: Breast tumor DNA T0173

value: Unknown


title: Breast tumor T0173_A


title: Donor 3


title: Donor 16


title: Donor 5


title: Breast tumor T0045_C

source_name: Breast tumor DNA T0045


title: Donor 10


title: timeseries sample175

value: sgRNA chr11

value: +shield


title: timeseries sample177

value: K562#17 clone with DD-Cas9 stably integrated


title: Breast tumor T0072_A


title: timeseries sample168


title: timeseries sample173

value: sgRNA AAVS1

value: -shield


title: Donor 6


title: Setd2D/D-rep2

city: Cincinnati

first: Gang

last: Huang

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description:
DEG_edgeR.txt
Expression_TPM.txt

data_processing:
A customized Perl script was employed to trim the bases with bad quality, which embed in read sequence.
Sequencing adaptor was removed using Cutadapt.
The trimmed RNA-seq data was subsequently mapped by RSEM to mm10, which downloaded from Ensembl database.
In the output of RSEM, TPM value was treated as normailized expression level and the expected counts for genes were used to calculated differentially expressed genes which were analyzed using edgeR. The adjsuted p-value was obatined based on Benjamini-Hochberg procedure.
Genome_build: mm10

source_name: Setd2D/D, Lin(-) Sca-1(+) c-Kit(+) cells

extract_protocol:
Total RNA was purifed using Rneasy microKit column system (QIAGEN）
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype

tag: age

value: 8-10 weeks

value: Lin(-) Sca-1(+) c-Kit(+) cells


title: timeseries sample169

source_name: K562 + DD-Cas9

value: sgRNA LBR2


title: timeseries sample172


title: Setd2D/D-rep1

description:
DEG_edgeR.txt
Expression_TPM.txt


title: Setd2f/f-rep1

description:
DEG_edgeR.txt
Expression_TPM.txt

source_name: Setd2f/f, Lin(-) Sca-1(+) c-Kit(+) cells


title: Setd2f/f-rep2

description:
DEG_edgeR.txt
Expression_TPM.txt


title: Breast tumor T0099_C

value: Female

value: Heterozygote

value: truncating variant


title: PK6-3: Ad-Cre PNPT1 fl/fl (PKO MEF) Clone 6 Replicate 3

city: Boston

first: Fasih

middle: Mubtasim

last: Ahsan

state: MA

address: 185 Cambridge Street, CPZN 6500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

data_processing:
PKO clones 1 and 6, rho0, and TM6 MEFs were each sequenced in biological triplicates (n = 3, 12 total samples). Raw sequencing reads were converted into fastq files and filtered for low quality reads and Illumina sequencing adapter contamination using bcl2fastq (Illumina). Trimmed reads were then aligned to the Mus musculus transcriptome, generated using the NCBI mm10 (NCBI/mm10/GRCm38, December 2011) genome and RefSeq gene annotation, using RSEM 1.2.25 prepare-reference (command parameters --bowtie --bowtie2 --gtf $(BUILD)/genes.gtf $(GENOME).fa $(RSEM)). Transcript counts were estimated using RSEM 1.2.25 calculate-expression, and collapsed to gene level counts using RSEM 1.2.25 tbam2gbam.  Gene-level transcript counts were extracted from the results output using custom R/3.4.1 scripts.
The resulting sample gene count matrix was size factor normalized and analyzed for pairwise differential gene expression using R/3.4.2 Bioconductor 3.6 package DESeq2 v1.18.1. Expression changes were estimated using an empirical Bayes procedure to generate moderated fold change values.  Significance testing was performed using the Wald test, and resulting P values were adjusted for multiple testing using the Benjamini-Hochberg procedure. DEGs were filtered using an adjusted false discovery rate (FDR) q value < 0.01 and an absolute log2 transformed fold-change > 0.5. Variance stabilized transform (VST) values in the gene count matrix were calculated and plotted for principal component analysis (PCA) using DESeq2. Scatterplots of gene expression fold-changes between TM6, rho0 and PKO MEFs were performed and Pearson/Spearman correlation coefficients calculated using R/3.4.1 package ggpubr v0.1.6 (https://cran.r-project.org/web/packages/ggpubr/index.html). Genes of interest were extracted and heat maps were prepared using R Bioconductor packages pheatmap v1.0.8 and gplots v3.0.1.
DEGs were extracted and analyzed for pathway/gene ontology (GO) term overrepresentation using the R/3.4.1 Bioconductor 3.6 package clusterProfiler v3.6.0 and ReactomePA v1.22.0, using a background gene set of all genes expressed with at least one read count in the sample gene count matrix. Overrepresented Reactome/KEGG pathways and GO terms were identified using significance testing cutoffs of P < 0.05, and an adjusted FDR < 0.25.
To determine overlapping significance between PKO and rho0 expression patterns relative to TM6, rank-rank hypergeometric overlap was performed using the online web server (http://systems.crump.ucla.edu/rankrank/rankranksimple.php).  Separate gene ranking lists were constructed according to the signed log10 transformed Wald test q value in fold change comparisons between PKO/TM6 and rho0/TM6. Hypergeometric testing was then performed to determine the significance of overlap between ranks in both datasets. Heat map values were plotted as the signed log10 transformed hypergeometric P value of overlap between ranks at the identified pixel; high values indicate enrichment of overlap, low values indicate reduced enrichment of overlap.
Genome_build: NCBI mm10
Supplementary_files_format_and_content: RSEM 1.2.25 calculate-expression gene level results .txt output ('Isoform', 'Chromosome', 'Strand', 'txStart', 'txEnd', 'cdsStart', 'cdsEnd', 'exonCount', 'exonStarts', 'exonEnds', 'Hugo', 'alignID', 'Canonical', 'length',  'effective_length', 'tx_expected_count', 'txTPM', 'txFPKM', 'IsoPct',  'gene_expected_count', 'geneTPM', 'geneFPKM')

source_name: PNPase KO TM6 MEF Clone 6

growth_protocol: Pnpt1fl/fl MEFs, named TM6, were grown at 37°C and 5% CO2 in Dulbecco’s Modified Eagle Medium supplemented with 10% Hyclone Fetal Bovine Serum (Thermo Scientific), 1X penicillin-streptomycin solution (Cellgro, Corning), and 50 μg/mL uridine (Sigma-Aldrich).  MEF rho0 cells were established by culturing with 750 ng/mL ditercalinium dichloride dihydrochloride (NCI DCTD Developmental Therapeutics Program, NSC 335153, NIH), for 3 weeks followed by single cell colony isolation.  PKO MEF lines were established by transduction of TM6 MEFs with a Cre-recombinase expressing adenovirus (SignaGen Laboratories cat # SL100707) in uridine- supplemented media, followed by isolation of single cell colonies.  Atoh1-Cre PKO mice were established by crossing Pnpt1fl/fl C57BL/6J mice with Atoh1-Cre transgenic C57BL/6J mice.

extract_protocol:
TM6, rho0 MEFs, and PKO clones were grown in biological triplicates to 70-80% confluence and purified using TriZol Reagent (Life Technologies) or RNeasy Mini Kit (Qiagen). All samples used showed a A260/280 ratio > 2.00 (Nanodrop; Thermo Scientific).
Strand-specific ribosomal RNA (rRNA) depleted RNA-Seq libraries were prepared from 1 µg of total RNA using the KAPA Stranded RNA-Seq Kit with Ribo-Erase (Kapa Biosystems, Roche). Briefly, rRNA was depleted from total RNA samples, the remaining RNA was heat fragmented, and strand-specific cDNA was synthesized using a first strand random priming and second strand dUTP incorporation approach. Fragments were then A-tailed, adapters were ligated, and libraries were amplified using high-fidelity PCR. All libraries were prepared in technical duplicates per sample (n = 12 samples, 24 libraries total), and resulting raw sequencing reads merged for downstream alignment and analysis. Libraries were paired-end sequenced at 2x125bp on an Illumina HiSeq.

value: Pnpt1 neo-flox/neo-flox

tag: treatment

value: Adenoviral-Cre

value: Mouse embryonic fibroblasts


title: Breast tumor T0045_A

value: breast tumor


title: PK6-2: Ad-Cre PNPT1 fl/fl (PKO MEF) Clone 6 Replicate 2


title: timeseries sample167


title: PK6-1: Ad-Cre PNPT1 fl/fl (PKO MEF) Clone 6 Replicate 1


title: PK1-3: Ad-Cre PNPT1 fl/fl (PKO MEF) Clone 1Replicate 3

source_name: PNPase KO TM6 MEF Clone 1


title: timeseries sample165


title: timeseries sample164


title: timeseries sample163


title: PK1-2: Ad-Cre PNPT1 fl/fl (PKO MEF) Clone 1Replicate 2


title: PK1-1: Ad-Cre PNPT1 fl/fl (PKO MEF) Clone 1 Replicate 1


title: timeseries sample162

value: +shield +NU7441


title: R0-1: DC-Treated PNPT1 fl/fl (rho0 MEF) Replicate 1

source_name: mtDNA deficient TM6 MEF


title: TM6-2: PNPT1 fl/fl WT (TM6 MEF) Replicate 2

source_name: wildtype TM6 MEF


title: R0-3: DC-Treated PNPT1 fl/fl (rho0 MEF) Replicate 3


title: timeseries sample170

value: -shield +NU7441


title: timeseries sample166

value: sgRNA chr11


title: timeseries sample161

value: -sgRNA

value: +shield


title: timeseries sample160

value: K562#17 clone with DD-Cas9 stably integrated


title: timeseries sample181

value: sgRNA AAVS1


title: timeseries sample158


title: 7134_wt_4C_rep2

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description: processed data file: 7134_wt_4C.bedGraph

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Gro-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50 --trim5 2
Gro-Seq_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
Gro-Seq_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragemnt and low quality reads (MAPQ <30)
HiC-Seq: generate contact matrix: juicer runnning with default parameter
4C-Seq: filtering: each read pair was tested for the presence of a perfect match to the respective bait primer as well as the bait spacer  between the  end of the primer and the restriction sites  used  in  the  corresponding  experiment.
4C-Seq: mapping: bowtie-1.1.1/bowite -X 500 -p 3 -v2 -k2 -m1 --phred64-quals -sam
4C-Seq: frequency: assign to DPNII/CSP6i fragment to calculate fraction of restriction fragments for which 4C reads were found
ChIAPET: followed the process described in Li et al.,2010
ChIAPET: interaction call by chiapettool v2 program with default parameter
ChIA-PET: Chia-PET processing pipeline is described in greater detail in Li et al., 2010 (PMCID: PMC2872882)
local HiC: preprocess & normalization: juicer.sh using default parameter
local HiC: 5kb resolution matrices extraction: juicebox dump obsevered NONE .hic BP 5000
local HiC: R & custom script: generate genome wide contact matrix as in Sanborn et al. PNAS 2015
local HiC: estimation of number of in silico spike-ins: median of the genome-wide per-bin coverage of the local HiC matrix at the targeted region
local HiC: reconstruct HiC matrix: combine the targeted region local HiC with the global CH12 wt matrix which matched to spike-ins
local HiC: re-normalization: Knight-Ruiz balancing algorithm with the juicebox pre -r 5000
ChromRNA_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChromRNA_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
ChromRNA_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content:
ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Gro-Seq: .wig files tag density divided by library size in millions to obtain normalized read density (rpkm)
HiC-Seq: .hic format including contact matrix, normalization information generated by juicer.sh
ChIAPET: bed12 format by editting the result of chiapettool by restricting to show only interactions having more than or equal to 3 PETs
4C-Seq: bed file showing read frequency in 100K window normalized by the number of fragments in each window
mRNA-Seq:.wig files tag density divided by library size in millions to obtain normalized read density (rpkm)
ChromRNA: strand-specific density tracks are generated by using bedtools genomecov program divided by library size in millions to obtain normalized read density (rpm)

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at 37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. MNase-Seq: 4x107 resting and activated B cells were digested with 24 different concentrations of MnaseI. After an initial RT-qPCR analysis and curve-fitting, the MnaseI concentrations for the most representative nucleosomal fraction was determined. The lowest three nucleosomal fractions (which corresponded to MnaseI concentrations of 0U, 0U, and 0.0026U) were pooled together and used as input control. Nucleosomal fractions 16-18 (which corresponded to enzyme concentrations of 0.068U, 0.045U, and 0.03U) were also pooled for further processing. Input samples were sonicated to obtain similar fragment sizes as the MnaseI-digested samples. DNA was then concentrated and each sample was spiked with 0.055mg of l DNA (also sonicated to match the sample size as was input DNA).
HiC-Seq: we used the same protocol for in situ HiC libraries at Rao et al., (Cell, 2014 Dec; 159:1-16)
Gro-seq: Nuclei was extracted from 8-12 million cells grown on 10 cm plates and after run-on reaction the RNA was extracted with Trizol LS Reagent (Invitrogen, Carlsbad, CA, USA). RNA was treated with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and purified by running through P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was dephosphorylated with PNK (New England Biolabs, Ipswich, MA, USA) followed by heatinactivation. Dephosphorylation reactions were purified using anti-BrdU beads (SantaCruz Biotech, Santa Cruz, CA, USA) and precipitated overnight. Poly(A)-tailing and cDNA synthesis was performed the next day as described in (Wang et al., 2011). However, for reverse transcription oligos with custom barcodes (underlined) were used : 5’-Phos CA/TG/AC/GT GATCGTCGGACTGTAGAACTCT /idSp/CAAGCAGAAGACGGCATACGA TTTTTTTTTTTTTTTTTTTTVN-3'. After cDNA synthesis, Exonuclease I (New England Biolabs; 30 min) was used to catalyze the removal of excess oligo. Enzyme was inactivated and RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA fragments of were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen). The recovered cDNA was circularized, linearized, amplified for 10-14 cycles. The final product was ran on Novex 10%TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit (Zymo Research Corporation, Irvine, CA, USA).
4C-seq: The 4C assay was performed as previously described van de Werken et al. (2012) with minor modifications. Ten million of CH12 B cell line were crosslinked in 2% formaldehyde at 37°C for 10 min. The reaction was quenched by the addition of glycine (final concentration of 0.125 M). Cells were then washed with cold PBS and lysed (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40, 1× complete protease inhibitors [Roche]) at 4°C for 1 hr. Nuclei were incubated at 65°C for 30 min, 37°C for 30 min in 500 μl of restriction buffer (New England BioLabs DpnII buffer) containing 0.3% SDS. To sequester SDS, Triton X-100 was then added to a final concentration of 1.8%. DNA digestion was performed with 400 U of DpnII (New England Biolabs) at 37°C overnight. After heat inactivation (65°C for 30 min), the reaction was diluted to a final volume of 7 ml with ligation buffer containing 100 U T4 DNA Ligase (Roche) and incubated at 16°C overnight. Samples were then treated with 500 μg Proteinase K (Ambion) and incubated overnight at 65°C to reverse formaldehyde crosslinking. DNA was then purified by phenol extraction and ethanol precipitation. For circularization, the ligation junctions were digested with Csp6I (Fermentas) at 37°C overnight. After enzyme inactivation and phenol extraction, the DNA  was  religated  in  a  7 ml  volume  (1,000 U  T4  DNA  Ligase,  Roche).  Three micrograms of 4C library DNA was amplified with Expand Long template PCR System (Roche). Thermal cycle conditions were DNA denaturing for 2 min at 94°C, followed by 30 cycles of 15 s at 94°C, 1 min at 58°C, 3 min at 68°C, and a final step of 7 min at 68°C.  Bait was amplified with inverse PCR primers as follows: 3RR with DpnII:_4C 5'-GCTTATCTGTAAAGAATGGGTC-3', 3RR_Csp6i 5'-GGCCTTAGAAGGCTCTGTAC-3'. 4C-amplified DNA was microsequenced with the Illumina platform.
mRNA-seq: Total RNA from 106 of WT or ZF9-11 CH12 cells was isolated by Trizol extraction. mRNA was then isolated .
local Hi-C: 500ng of Hi-C library (8 cycles of amplification) was mixed with 2.5 µg of mouse Cot-1 DNA and 10µg of salomon sperm DNA in a total volume of 25µl. The sample was heated to 95℃ for 5 minutes. Next the temperature was diminished to 65℃ and the samples incubated for at least 5 minutes at 65℃. In the meantime 6µl of a RNA probe mixture (500ng of RNA probes, 20U of supreRNAseIn) and 33µl of hybridization buffer (10xSSPE, 10xDenhardt buffer, 10mM EDTA, 0.2% SDS) were incubated at 65℃. Next, the hybridization buffer and the RNA probe mixture were added to the sample. The final mix was incubated at 65℃ for 24 hours. Following the hybridization, 50 µl of MyOne Streptavidin T1 beads were washed 3 times with Bind-and-Wash buffer (1M NaCl, 10 mM Tris-HCl, pH=7.5, 1mM EDTA) and then resuspended in 134 µl of Bind-and-Wash buffer and added to the sample. The mixture was incubated for 30 minutes at room temperature with occasional swirling. Next, beads were separated using a magnet and the supernatant discarded. Beads were then washed once with 200µl of low-stringency buffer (1xSSC, 0.1%SDS) and incubated for 15 minutes at RT. Beads were separated and washed 3 times with high stringency.
ChromRNA-seq: chromatin RNA fraction was prepared from 3*10^6 cells following the method previously described (Pandya-Jones & Black, RNA, 2009) with some modifications. The pellet was lysed in a cytoplasm lysis buffer (20mM Hepes-KOH pH 7.6, 2mM MgCl2, 10% glycerol, 0.1% NP40, 0.5mM DTT with protease inhibitor, phosphatase inhibitor and RNase inhibitor). The lysate was then layered on top of a sucrose buffer in order to isolate the nuclei fraction from the cytoplasmic one (10mM Hepes-KOH pH7.6, 10mM NaCl, 1.5mM MgCl2, 10% glycerol, 0.5mM EDTA, 0.5mM DTT, 34% sucrose w/v with protease inhibitor, phosphatase inhibitor and RNase inhibitor).
ChromRNA-seq: The nuclei fraction was resuspended and lysed in a nuclear lysis buffer (10mM Hepes-KOH pH 7.6, 100mM NaCl, 0.5mM EDTA, 50% glycerol, 0.5mM DTT with protease inhibitor, phosphatase inhibitor and RNase inhibitor). Chromatin was precipitated by adding a Urea c

tag: cell line

value: Tumor 7134 cell

tag: genotype/variation

value: WT

value: lymphoma cell line


title: 7134_wt_4C_rep1


title: timeseries sample157


title: TM6-1: PNPT1 fl/fl WT (TM6 MEF) Replicate 1


title: 7134_SAd_4C_rep2

description: processed data file: 7134_SAd_4C.bedGraph

value: SA deletion


title: 7134_SAd_4C_rep1


title: R0-2: DC-Treated PNPT1 fl/fl (rho0 MEF) Replicate 2


title: timeseries sample156


title: timeseries sample155


title: mouse bone GFP+(lo) rep2

city: stanford

first: Hui

last: Zhu

address: 1651 Page Mill Road

institute: Stanford Universtiy

data_processing:
Paired end sequencing reads (100bp) were generated and aligned to the mouse reference sequence NCBI Build 37/mm9 with the STAR (v2.4.2a) algorithm.
Normalization of RefSeq annotated gene expression level and differential expression analysis were performed using Bioconductor package DESeq2 in R (Version 3.2.2)
rlog-transformed values (the regularized-logarithm transformation for count data) was calculated for each gene.
Genome_build: mm9
Supplementary_files_format_and_content: basemean count measurement

source_name: Col2.3GFP transgenic mouse

growth_protocol: mESCs and iPSCs were maintained in either ESC medium on MEF feeder cells or in feeder free condition in serum free ESC medium.

extract_protocol:
RNA was extracted with the PureLink® RNA Mini Kit, and purified using the Dynabeads® mRNA Purification Kit. For ultra-low amounts of RNA, RNA was extracted using the NucleoSpin® RNA XS kit
RNA sequencing libraries were generated from purified mRNA using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. For ultra-low amounts of RNA, libraries were prepared with the SMART-Seq v4 Ultra Low Input RNA Kit followed by the Low Input Library Prep Kit.

treatment_protocol:
Dissociated mouse Col2.3GFP ESCs and Col2.3GFP iPSCs were cultured as EBs in suspension in 6 well ultra-low cluster plates for 6 days with ESC medium or serum free ESC medium without LIF, PD0325901 and CHIR99021.  0.1 μM retinoic acid (RA) was added at day 3 and washed out at day 5.  After 6 days, EBs were plated in osteogenesis medium.
The calvarial osteoblasts were maintained and matured in αMEM medium containing 10 % FBS and 1× penicillin-streptomycin and supplemented with 50 μg/mL ascorbic acid.

value: GFP positive cells sorted from mouse long bone

tag: age or differentiation days

value: post natal day 23


title: mouse bone GFP+(lo) rep3


title: mouse bone GFP+(hi) rep2


title: TM6-3: PNPT1 fl/fl WT (TM6 MEF) Replicate 3

value: Pnpt1 neo-flox/neo-flox


title: mouse bone GFP+(lo) rep1


title: timeseries sample159


title: iPSC rep2

source_name: Col2.3GFP miPSC line

value: passage 10-20 miPSCs

value: differentiation for 0 day


title: timeseries sample154


title: timeseries sample153

value: sgRNA LBR2


title: mouse bone GFP+(hi) rep1


title: iPSC rep1


title: mouse bone GFP+(hi) rep3


title: timeseries sample151


title: timeseries sample152

value: -shield


title: timeseries sample150


title: ESC-OB rep3

source_name: Col2.3GFP mESC line

value: passage 20-30 mESCs differentiated to osteoblast cells

value: differentiation for 35-40 days


title: ESC rep1

value: passage 20-30 mESCs


title: iPSC-OB rep2

value: passage 10-20 miPSCs differentiated to osteoblast cells


title: ESC rep3


title: ESC rep2


title: timeseries sample148

value: K562#17 clone with DD-Cas9 stably integrated

value: sgRNA chr11

value: +shield


title: ESC-OB rep2


title: ESC-OB rep1


title: ESC-OB-GFPplus_rep2

value: GFP positive cells sorted from mESC differentiated osteoblast cells


title: iPSC-OB rep1


title: ESC-OB-GFPplus_rep3


title: calvarial-OB rep2

source_name: calvarial osteoblast cells

value: calvarial osteoblast cells differentiated to mature osteoblast cells

value: differentiation for 3 weeks


title: timeseries sample149


title: calvarial-OB rep3


title: timeseries sample145

value: sgRNA AAVS1


title: timeseries sample143


title: timeseries sample146


title: timeseries sample141


title: timeseries sample142


title: timeseries sample138


title: timeseries sample137


title: timeseries sample144

value: +shield +NU7441


title: timeseries sample139


title: timeseries sample140


title: timeseries sample132


title: timeseries sample133


title: timeseries sample134


title: timeseries sample135


title: timeseries sample136


title: ESC-OB-GFPplus_rep1


title: timeseries sample147


title: timeseries sample128


title: timeseries sample131


title: timeseries sample129


title: timeseries sample130


title: timeseries sample126


title: timeseries sample125


title: timeseries sample124


title: timeseries sample123


title: calvarial-OB rep1


title: timeseries sample122


title: timeseries sample119


title: timeseries sample120


title: timeseries sample118


title: timeseries sample116


title: timeseries sample112


title: timeseries sample114


title: timeseries sample110


title: timeseries sample111


title: timeseries sample127


title: timeseries sample109


title: timeseries sample108


title: timeseries sample115


title: esc_wt_mRNA_rep3

description: mRNA-Seq

source_name: ES cell

treatment_protocol: Myc floxed allele was obtained from Douglas Green (St. Jude Children’s research hospital). Myc flox/flox mice (WT) or RosaCreERTam/Myc flox/flox mice (KO) were treated with tamoxifen (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice). The deletion of floxed allele was checked by PCR or intracellular staining of Myc protein.

value: WT

value: blastocyst


title: timeseries sample107

value: -sgRNA


title: timeseries sample121


title: ch12_CTCFZF9to11_mRNA_rep5

description:
mRNA-Seq
ch12_CTCFZF9to11_mRNA_merged.bw

source_name: CH12 B cell line

value: lymphoma cell line


title: timeseries sample105

value: sgRNA LBR2


title: ch12_ZF9to11_Rad21_rep2

tag: chip antibody

value: Anti-Rad21 (abcam; ab992)


title: ch12_wt_CTCF_rep1

value: anti-CTCF (EMD Millipore; 07-729)


title: ch12_wt_CTCF_rep3


title: ch12_wt_CTCF_rep2


title: esc_wt_mRNA_rep1

description: mRNA-Seq


title: timeseries sample117


title: timeseries sample104


title: esc_wt_CTCF_rep2


title: ch12_wt_Rad21_rep5


title: ch12_ZF9to11_Rad21_rep1


title: ch12_wt_Rad21_rep6


title: timeseries sample113

value: -shield


title: timeseries sample102


title: ch12_wt_Rad21_rep3


title: esc_wt_mRNA_rep2

description: mRNA-Seq


title: ch12_wt_Rad21_rep2


title: timeseries sample106


title: ch12_wt_Rad21_rep1


title: ch12_ZF9to11_Rad21_rep3


title: timeseries sample101


title: timeseries sample100


title: timeseries sample99


title: timeseries sample103


title: ch12_ZF9to11_ChIAPET


title: Kir4.1cKO_Astrocyte_S5

city: San Francisco

first: Kevin

middle: William

last: Kelley

state: CA

address: 35 Medical Center Way

institute: UCSF

data_processing:
Read quality was assessed using fastqc v0.11.4 and the first 5 bases as well as the last base of each read was trimmed and aligned to the Mus Musculus genome (Ensembl GRCm38) using TopHat2 v2.0.11 with bowtie2 v2.2.3.
TopHat2 was run with the following arguments “--no-coverage-search --segment-mismatches 1” with the genes.gtf file from Ensembl GRCm38.
Gene counts were created from the alignment files using htseq-count v0.6.1p1 with default parameters.
From raw count files, DESeq2 v1.14.1 was used to detect differentially expressed genes
FPKM values were generated using cuffquant and cuffnorm from cufflinks v2.2.1
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample; FPKM values are provided as comma-separated values; DESeq2 output provided as comma-separated values

source_name: spinal cord

extract_protocol:
Spinal cords were dissected. Meninges were removed, then dissociated with papain (20 U ml-1, Worthington) for 80min at 33°C. Aldh1l1-GFP+  cells were FACS sorted.
Total RNA was extracted with Trizol (Invitrogen) and purified using the RNeasy Kit (Qiagen). cDNA was generated from full length RNA using the NuGEN RNA-Seq V2 kit.

value: spinal cord astrocytes

value: mixed swiss-webster

value: spinal cord


title: Kir4.1cKO_Astrocyte_S4


title: Kir4.1cKO_Astrocyte_S3


title: WT_Astrocyte_S7


title: ch12_wt_Rad21_rep4


title: timeseries sample97

value: K562#17 clone with DD-Cas9 stably integrated

value: +shield


title: WT_Astrocyte_S6


title: timeseries sample96


title: timeseries sample98

value: -shield +NU7441


title: WT_Astrocyte_S2


title: AtT-20 iPAM cells, induced 'H'

city: Farmington

first: Richard

middle: E

last: Mains

state: CT

address: 263 Farmington Ave, Neuroscience Dept., Neuroscience Dept.

department: Neuroscience

institute: University of Connecticut Health Center

data_processing:
Base calling and quality scores using RTA 2.1.3 from NextSeq control software 1.3.0.23
Reads were aligned to mm10 using Bowtie v. 2.1.0.0 and Samools v. 0.1.19.0
Exon-exon splice junctions were identified using Tophat v. 2.0.9
Transcriptome assembly and quantification of expression was performed with Cufflinks v. 2.2.0
Differential expression analyzed using Cuffdiff 2.2.0, DESeq2 and Limma
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: corticotrope tumor line

growth_protocol: serial passage in DMEM-F12 with 10% FBS, Pen-Strep, G418 and hygromycin.

extract_protocol:
Dense wells of a 6-well dish were extracted in Trizol and processed as per manufacturer's instructions
AmpliSeq™ Library PLUS per manufacturer's instructions
RNASeq samples were barcoded and all run in a single lane with 16.6 million reads per sample.

treatment_protocol: Induced cells received 4 micrograms/ml doxycycline for 48h before extraction.

tag: expression

value: PAM induced


title: WT_Astrocyte_S1

tag: cell type


title: timeseries sample95

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

data_processing:
Library strategy: DNA-Seq
Mutation identification: In each sequence read, the distance between a fixed sequence at the start and at the end are determined and used to calculate a score, defined as the difference between the measured distance in the read and the expected distance in a wild-type sequence. Insertions and deletions have score >0 and <0, respectively. A point mutation has score=0, but some bases in the sgRNA target site differ from the wild-type sequence. The intact type specifies reads identical to wild-type sequences.   Per time point, the ratio of each type over the total of reads is calculated. We observed only 2 - 6.5% sequence reads in which we could not find a match with the constant parts and we discarded these reads in subsequent analyses. The called point mutations (score = 0) showed a very similar kinetic profile as the intact sequence (wild-type), indicating that they are mostly sequencing errors. We therefore assigned them as intact sequence in the analysis. Insertion and deletion levels at time point t = 0 h were considered as background and subtracted from all time points.  In the double-cut assays, paired end sequencing was performed. The forward and reverse read were matched by the unique sequence ID of a pair of reads. The deletion events were divided into two types: (i) perfectly excised DNA, and (ii) excised DNA with an indel when the deletion was larger than the expected excised product or up to 5 nucleotides smaller.
Supplementary_files_format_and_content: txt files with barcode, indel type, indel score, sequence; sum txt files with indel type, indel score of pool

extract_protocol:
Cells were collected by centrifugation (300xg, 5 min) and the genomic DNA was isolated using the Isolate II Genomic DNA Kit (Bioline).
PCR was performed in two steps; PCR1 with ~100 ng genomic DNA and site specific barcoded primers. PCR2 used 2 µL of each PCR1 product with Illumina PCR Index Primers Sequences 1–12. Each sample was generated with a unique combination of a barcode and index. Both PCR reactions were carried out with 25 µL MyTaq Red mix (Bioline), 4 µM of each primer and 50 µL final volume in a 96 well plate. PCR conditions were 1 min at 95 ˚C, followed by 15 sec at 95 ˚C, 15 sec at 58 ˚C and 1 min at 72 ˚C (15x). 20 µL of 8 samples were pooled and 100 µL was loaded onto a 1% agarose gel. PCR product was cut from gel to remove the primer dimers and cleaned with PCR Isolate II PCR and Gel Kit (Bioline).

tag: strain


title: AtT-20 iPAM cells, induced 'F'


title: AtT-20 iPAM cells, basal 'E'

value: PAM basal


title: timeseries sample93

tag: sgrna target site


title: timeseries sample94

tag: time point


title: AtT-20 iPAM cells, basal 'C'


title: AtT-20 iPAM cells, induced 'G'


title: HSC BRL37344 treated old rep3

city: Bronx

first: Paul

last: Frenette

state: NY

address: 1301 Morris Park Avenue , Room 101

department: Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research

institute: Albert Einstein College of Medicine

description: J703_AHW5G3BGXY_GGACTCCT-AGAGGATA_9-HSC-Y-S

data_processing:
Library adaptor sequences were trimmed using trim galore ( https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ )
Then reads were aligned to the mouse genome (mm10) using Spliced Transcripts Alignment to a Reference (STAR 2.5.3a)
Aligned reads were then quantified to transcriptome (mm10 - Ensembl Transcripts release 83), normalized and differentially expressed genes were identified using Partek Flow
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file contains gene counts for individual samples generated by Partek Flow

source_name: HSC BRL37344 treated old

extract_protocol:
Total RNA from ~2000 sorted HSCs was extracted using the RNAeasy Plus Micro kit (Qiagen), and assessed for integrity and purity using an Aligent 2100 Bioanalyzer (Agilent Technologies).
Complementary DNA libraries were then generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) and the Nextera XT DNA Sample preparation Kit (Illumina).

treatment_protocol: For long-term administration of β3-adrenergic agonist BRL37344 (Sigma) was dosed at 2.4 mg Kg-1 day-1, using subcutaneously implanted Alzet osmotic pumps (model 2006; DURECT Corporation) into young (2 month old) and old (15-20 month old) mice . Six weeks following implantation of the first pump, an additional pump was implanted for a total of 12 weeks of continuous drug delivery. Control animals were implanted with Alzet pumps containing saline (PBS; Gibco).

value: adult; old

tag: treated with

value: bone marrow

value: hematopoietic stem cells (HSCs)


title: ch12_wt_ChIAPET

value: WT


title: timeseries sample92

tag: time series + conditions

tag: conditions


title: HSC BRL37344 treated old rep2

description: J703_AHW5G3BGXY_TCCTGAGC-ATAGAGAG_8-HSC-Y-S

tag: tissue


title: HSC BRL37344 treated old rep1

description: J703_AHW5G3BGXY_TAAGGCGA-TCTACTCT_7-HSC-Y-S


title: timeseries sample91


title: Kir4.1cKO_Astrocyte_S8


title: HSC saline treated old rep3

description: J703_AHW5G3BGXY_TAGGCATG-AGAGGATA_6-HSC-Y-S

source_name: HSC saline treated old

value: saline


title: HSC saline treated old rep2

description: J703_AHW5G3BGXY_GGACTCCT-TCTTACGC_5-HSC-Y-S


title: HSC saline treated old rep1

description: J703_AHW5G3BGXY_TCCTGAGC-TCTACTCT_4-HSC-Y-S


title: HSC saline treated young rep3

description: J703_AHW5G3BGXY_AGGCAGAA-AGAGGATA_3-HSC-Y-S

source_name: HSC saline treated young

value: young adult


title: timeseries sample89

source_name: K562 + DD-Cas9

value: sgRNA LBR2


title: HSC saline treated young rep1

description: J703_AHW5G3BGXY_TAAGGCGA-TCTTACGC_1-HSC-Y-S


title: AtT-20 iPAM cells, basal 'D'


title: timeseries sample88


title: timeseries sample85


title: timeseries sample86


title: timeseries sample83


title: single cell RNAseq of pooled insulin+ pancreatic ductal cells and pancreatic β-cells SI-GA-G1_2

city: Ashburn

first: Yuhan

last: Wang

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

description: Insulin+ pancreatic ductal cells and pancreatic β-cells were collected from the pancreas after retrograde common bile duct delivery of adPNM. Both cell types were isolated through FACS and pooled as one sample for single cell RNA sequencing. Expression of adenoviral vector sequence was used to distinguish insulin+ pancreatic ductal cells from pancreatic β-cells.

data_processing:
Cell Ranger 2.0 Single-Cell Software Suite was used to demultiplex sequencing samples, align reads, and count UMI for single cells.
A custom reference file was created by adding a unique sequence contained in the adenoviral vector to GRCm38, and using Cell Ranger ‘mkref’ to construct a Cell Ranger-compatible reference.
Genome_build: GRCm38/mm10

source_name: pancreas

extract_protocol:
The pancreas from a Rag2-/-  MIPGFP animal was harvested two months after retrograde common bile duct injection of the AdPNM reprogramming vector. Cells were dissociated, isolated by FACS based on GFP expression and used for single-cell library preparation with the 10X Genomics Chromium system.
Single cell RNA-Seq libraries were prepared using the GemCode Single Cell 3′ v2 reagent kit (10X Genomics). Sequencing libraries were loaded on an Illumina NextSeq 500 with 2 × 75 paired-end reads.

value: pooled insulin+ pancreatic ductal cells and pancreatic beta-cells


title: single cell RNAseq of pooled insulin+ pancreatic ductal cells and pancreatic β-cells SI-GA-G1_3


title: single cell RNAseq of pooled insulin+ pancreatic ductal cells and pancreatic β-cells SI-GA-G1_4


title: timeseries sample82


title: timeseries sample81

value: +shield +NU7441


title: timeseries sample79


title: timeseries sample78


title: timeseries sample80


title: timeseries sample84


title: FACS086_9_A05

city: Menlo Park

first: Thomas

last: Portmann

address: 1505 O'Brien Dr

department: Neurobiology and Transcriptomics

institute: Circuit Therapeutics

description: SMARTer Ultra Low Input RNA Kit for Sequencing – v3

data_processing:
Illumina BCL files were converted and demultiplexed (bcl2fastq 2.18) using default parameters
A custom mouse reference genome was created by adding EGFP and tdTomato sequences to the mouse reference genome mm10/ GRCm38 and gene annotation version GRCm38.75. Gpr52 added to confirm previous findings
Fastq files were aligned to the custom mouse reference genome (STAR 2.5.0).
Sequencing and RNA quality control reports were generated (FastQC 0.11.5 and Qualimap 2.2.1)
Aligned reads were summarized as gene-level counts (featureCounts 1.5.1).
Pairwise differential expression was conducted between groups with the R package DESeq2 (v1.14.1).
Genome_build: genome mm10/ GRCm38 and gene annotation version GRCm38.75

source_name: dorsomedial striatum_Drd1

extract_protocol:
as described in Ho, De Both et al.
as described in Ho, De Both et al.

value: adult brain, dorsomedial striatum


title: FACS086_9_A12

source_name: dorsomedial striatum_Drd2


title: FACS086_9_A06


title: timeseries sample77


title: FACS086_9_A04


title: timeseries sample90


title: HSC saline treated young rep2

description: J703_AHW5G3BGXY_CGTACTAG-ATAGAGAG_2-HSC-Y-S


title: timeseries sample76


title: timeseries sample87


title: FACS086_4_D12


title: single cell RNAseq of pooled insulin+ pancreatic ductal cells and pancreatic β-cells SI-GA-G1_1


title: FACS086_4_D11


title: FACS086_4_D07


title: timeseries sample75


title: FACS086_4_D03


title: timeseries sample74

value: -shield


title: FACS086_4_D08


title: FACS086_4_D04


title: FACS086_4_D01


title: timeseries sample73


title: timeseries sample72


title: FACS086_4_C12


title: FACS086_4_D02


title: FACS086_4_C11


title: timeseries sample71


title: timeseries sample70


title: FACS086_4_C09


title: FACS086_4_C08


title: homo4

city: Kurume

first: Michiyo

last: Tsuru

state: Fukuoka

address: 67 Asahimachi

department: Orthopardic Surgery

country: Japan

institute: Kurume Universuty

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Mouse Genome Microarray Kit; Agilent Technologies) according to the manufacturer's instructions.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: kidney

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

extract_protocol: Total RNA was prepared from cells using an AllPrep DNA/RNA Mini Kit (Qiagen), according to the manufacturer’s instructions.

value: kidney

value: knockout


title: FACS086_4_C07


title: FACS086_4_C06


title: timeseries sample69

value: K562#17 clone with DD-Cas9 stably integrated


title: FACS086_4_C05


title: wild54

value: wild type


title: FACS086_4_C04


title: FACS086_4_C03


title: timeseries sample68

value: -sgRNA

value: -shield +NU7441


title: FACS086_4_C02


title: FACS086_4_C01


title: timeseries sample67

value: +shield


title: FACS086_4_B11


title: FACS086_4_B12


title: timeseries sample66


title: FACS086_4_B08


title: timeseries sample64


title: FACS086_4_B06


title: FACS086_4_B09


title: FACS086_4_B07


title: FACS086_4_B05


title: timeseries sample65


title: FACS086_4_B10


title: FACS086_4_B04


title: timeseries sample63


title: timeseries sample62


title: timeseries sample61


title: FACS086_4_B02


title: timeseries sample59


title: FACS086_4_A12


title: FACS086_4_A06


title: FACS086_4_A11


title: timeseries sample58


title: FACS086_4_A05


title: FACS086_4_A04


title: timeseries sample57


title: timeseries sample60


title: timeseries sample56


title: FACS086_4_A01


title: FACS086_4_A07


title: FACS086_4_A02


title: FACS051_5_D02


title: FACS051_5_C10


title: timeseries sample55


title: FACS051_5_C08


title: timeseries sample54


title: FACS051_5_C12


title: FACS086_4_B01


title: FACS086_4_B03


title: FACS051_5_D04


title: caBmpr1a Rep #3

city: Durham

first: Yoshihiko

last: Kobayashi

state: NC

address: 307 Research Dr

department: Cell Biology

institute: Duke University

data_processing:
Paired-end sequencing (150 bp for each read) was performed using HiSeq X with the depth of 24 million reads for each sample. Quality of sequenced reads were assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). PolyA/T tails were trimmed using PRINSEQ (Schmieder and Edwards, 2011). Adaptor sequences were trimmed and shorter reads than 24 bp were dropped using Trimmomatic (Bolger et al., 2014). Reads were mapped to the mouse reference genome (mm10) using Hisat2 (Kim et al., 2015) with default setting. Duplicate reads were removed using the markdup option of SAMtools (Li et al., 2009). Fragments numbers were counted using the featureCounts option of SUBREAD (Liao et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: TXT, counted fragment numbers using featureCounts

molecule: polyA RNA

source_name: Alveolar type II cells

extract_protocol:
Total RNA was isolated from FACS-sorted cells using TRIzol (Thermo Fisher Scientific) and Direct-zol RNA MicroPrep (Zymo Research).
Messenger RNA was enriched from 200 ng of isolated total RNA of each sample using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs).

value: 12 weeks old


title: FACS051_5_C07


title: FACS086_4_A09


title: FACS051_5_C06


title: timeseries sample52


title: timeseries sample53


title: caBmpr1a Rep #2


title: caBmpr1a Rep #1

value: 16 weeks old


title: FACS051_5_C04


title: timeseries sample51


title: Control Rep #3

value: Sftpc-CreERT2/+; R26-tdTomato/+


title: FACS051_5_C02


title: FACS051_5_C03


title: FACS051_5_D01


title: FACS051_5_C01


title: Control Rep #2


title: FACS051_5_B12


title: Control Rep #1


title: FACS051_5_B11


title: timeseries sample49


title: timeseries sample48


title: timeseries sample47


title: timeseries sample50


title: FACS051_5_B10


title: FACS051_5_B09


title: timeseries sample46


title: FACS051_5_C05


title: FACS051_5_B06


title: timeseries sample45


title: FACS051_5_B05


title: FACS051_5_B07


title: FACS051_5_B03


title: FACS051_5_B02


title: timeseries sample44


title: FACS051_5_A12


title: timeseries sample43


title: FACS051_5_B01


title: FACS051_5_A11


title: FACS051_5_A10


title: timeseries sample42


title: FACS051_5_B08


title: FACS051_5_A09


title: timeseries sample41


title: FACS051_5_A08


title: timeseries sample40


title: alg-2 rep3

city: La Jolla

first: Amy

last: Pasquinelli

address: 9500 Gilman Drive

department: Biological Sciences

institute: University of California, San Diego

description:
alg-2 AD5 rep3
alg-2(ok304) vs WT AD5

data_processing:
Basecalling with Illumina's software RTA2
mapping of sequencing reads to the C. elegans genome (ce10) was performed using RNA-STAR
Total read counts for each gene were then quantified using HTSeq
These read counts were then input into DESeq to determine log2-fold change and differential expression between the mutant and WT strains
Genome_build: ce10
Supplementary_files_format_and_content: excel files were gemerated using DeSeq determine log2-fold change and differential expression between the mutant and WT strains

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Synchronized WT, alg-1(gk214) and alg-2(ok304) animals cultured at 20°C were collected at adult day 5 after removing eggs and progeny larvae.

extract_protocol:
RNA was extracted with Trizol and DNAse treated
Libraries were prepared according to Illumina's TruSeq RNA (15031048 Rev. D). Briefly ribsomal RNA was depleted, adpaters ligated, library amplified, purified and validated.

treatment_protocol: No special treatment

tag: developmental stage

value: adult day 5 (D5)


title: alg-1 rep3

description:
alg-1 AD5 rep3
alg-1(gk214) vs WT AD5

tag: genotype


title: FACS051_5_A07


title: FACS051_5_B04


title: timeseries sample39


title: FACS051_5_A05


title: alg-1 rep2

description:
alg-1 AD5 rep2
alg-1(gk214) vs WT AD5


title: FACS051_5_A04


title: N2 rep3

description:
N2 AD5 rep3
alg-1(gk214) vs WT AD5 & alg-2(ok304) vs WT AD5

value: N2 (WT)


title: N2 rep2

description:
N2 AD5 rep2
alg-1(gk214) vs WT AD5 & alg-2(ok304) vs WT AD5


title: alg-2 rep1

description:
alg-2 AD5 rep1
alg-2(ok304) vs WT AD5


title: FACS051_5_A03


title: FACS051_5_A02


title: timeseries sample36

value: sgRNA LBR2


title: alg-1 rep1

description:
alg-1 AD5 rep1
alg-1(gk214) vs WT AD5


title: timeseries sample35


title: timeseries sample37


title: timeseries sample34


title: N2 rep1

description:
N2 AD5 rep1
alg-1(gk214) vs WT AD5 & alg-2(ok304) vs WT AD5


title: FACS051_5_A01


title: alg-2 rep2

description:
alg-2 AD5 rep2
alg-2(ok304) vs WT AD5


title: timeseries sample38


title: timeseries sample32