title: CLOCK defecient hMSCs  rep 1 [RNA-Seq]

first: ji

middle: qian

last: zhao

address: 15 Datun Road Chaoyang District

institute: institute of zoology ,CAS

description: RNA-seq of CLOCK deficient hMSCs.

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2 or histat2 software.
Genome_build: hg19 for Homo sapiens and mm10 for Mus musculus data.
Supplementary_files_format_and_content: Txt file of read count for RNA-seq. bw file fof RPKM normalized read cout for each 10 bp bin size for others sequencing data.

source_name: Mesenchymal stem cell

growth_protocol: Human MSCs (hMSCs) were cultured in MEMa (Thermo Fisher Scientific) medium supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific (Cat:10099-141, Lot:1616964)), 0.1 mM non-essential amino acids (Thermo Fisher Scientific), 1% penicillin/streptomycin (Thermo Fisher Scientific), and 1 ng/ml bFGF (Joint Protein Central, Incheon, Korea).

extract_protocol:
For DamID-seq, genomic DNA were isolated using DNeasy Blood & Tissue Kit (Qiagen). For ChIP-seq, DNA was isolated sing phenol-chloroform-isoamylalcohol extraction and ethanol precipitation. For RNA-seq, total RNA was extracted in TRIzol (Thermo Fisher Scientific) and genomic DNA was removed using a DNA-free kit (Thermo Fisher Scientific)
For ATAC-seq, library amplified and purified using TruePrep DNA Library Prep Kit V2 for Illumina(Vazyme Biotech). For DamID-seq, the DNA library was constructed using aNEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. For ChIP-seq, the enriched fragments were constructed into libraries without the incorporation of spike-in controls via KAPA Hyper Prep Kits with PCR Library Ampliﬁcation/Illumina series (KK8504) following the manufacturer’s instructions. For RNA-seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: Mesenchymal stem cell

tag: genotype

value: CLOCK defecient hMSCs


title: SW480 Clone1

status: Public on Feb 11 2020

type: RNA

city: Shenyang

first: Yong

last: Zhou

state: Liaoning

address: 4 Chongshan Road

country: China

institute: the Fourth Affiliated Hospital of China Medical University

description:
Control
long non-coding RNAs
SAMPLE 1

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://geneglobe.qiagen.com/cn/analyze/
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1, RPLP0.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change data file reports test/control (SW480R/SW480) ratios.

label: SYBR Green

molecule: total RNA

organism: Homo sapiens

source_name: SW480 Clone1

label_protocol: RT2 lncRNA qPCR Assay were performed using the Custom RT2 PCR Arrays (QIAGEN, Hilden, Germany) following the Manufacturer’s instructions. 1 mg RNA was reverse transcribed to cDNA in 20μl system by First Strand cDNA Synthesis Kit for RT-PCR (Merck & Co., Inc., Kenilworth, NJ, USA). Real-time PCR was performed using the Mx3000P real-time PCR system (Thermo Fisher Scientific, Waltham, MA, USA). PCR was carried out as follows: 40 cycles of 94 °C for 15s, 60 °C for 10s and 72 °C for 20s.

growth_protocol: SW480 obtained from American Type Culture Collection (Manassas, VA, USA) and was exposed to stepwise increasing Regorafenib for over 12 months. The survival cells were subsequently passaged and grew under the same conditions for more than 20 passages with 0.02μM Regorafenib. The regorafenib-adapted cells were termed SW480R. Cells were grown in RPMI-1640, supplemented with 10% FBS. All cell lines were maintained in a humidified incubator with 5% of CO2 and 95% air at 37°C.

extract_protocol: Total RNA was extracted by 1 mL TRIzol (Merck & Co., Inc., Kenilworth, NJ, USA)according to the manufacturer’s protocol.

tag: cell line

tag: phenotype

value: parental cell line (passage 0)

tag: tissue

value: colon cancer cell


title: CLOCK defecient hMSCs  [ChIP-Seq]

type: SRA

city: Beijing

description:
Input file corresponding to H3K9me3 ChIP-seq data of CLOCK deficient hMSCs.
H3K9me3_CLOCK.bin_10.bw

library_source: genomic

molecule: genomic DNA

tag: cell type

tag: passage


title: WT hMSCs  rep 2 [RNA-Seq]

description: RNA-seq of WT hMSCs.

library_source: transcriptomic

value: WT hMSCs


title: WT hMSCs  rep 1 [RNA-Seq]

description: RNA-seq of WT hMSCs.


title: CLOCK defecient hMSCs  rep 2 [RNA-Seq]

description: RNA-seq of CLOCK deficient hMSCs.


title: WT hMSCs rep 1 [ChIP-Seq]

description:
H3K9me3 ChIP-seq of WT hMSCs.
H3K9me3_WT.bin_10.bw


title: D17_2: donor_17_rep 2

city: Nizhny Novgorod

first: Dmitry

last: Knyazev

address: Malaya Yamskaya, 71

country: Russia

institute: I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology

hyb_protocol: Fragmented labeled RNA (2 ug) was hybridized at 40°C for 18-20 hours in Hyb-solution (6xSSPE, 20mM EDTA, 0,05% Tween-20, salmon sperm DNA 10 mg/ml, 0,04% SDS,  formamide 25%vol). Arrays were sequentially washed  by 3хSSPE, 0,05% Tween-20 → 0,5хSSPE, 0,05% ТTween20 → 2xPBS 0,1% Tween-20. Subsequent blocking, labeling, label wash, substrate solution treatment were fulfilled using ElectraSense Detection Kit (CustomArray Inc., WA, USA)

scan_protocol: Amperometric signal measurements were performed using ElectraSense Reader device and ElectraSense application software (CustomArray Inc., WA, USA)

data_processing: Feature data from .ecd-files was exported to csv.-files using ElectraSense Analysis 3.4.2. All further calculations were performed in R (version 3.5.0, The R Foundation for Statistical Computing, Inc) using RStudio software (version 1.1.453, RStudio, Inc). Background correction was made using RMA. Data were normalized using the subset quantile normalization based on the non-specific control features (Wu Z., Aryee M.J. Subset Quantile Normalization Using Negative Control Features. J Comput Biol 2010; 17(10): 1385-1395, https://doi.org/10.1089/cmb.2010.0049).

label: biotin

source_name: peripheral blood leukocytes

label_protocol: 1. Total RNA (1,5-2 ug) was converted to T7-promoter-containing cDNA by Mint cDNA synthesis kit (Evrogen, Russia, http://evrogen.ru/technologies/Mint-cDNA-synthesis.shtml), kit' 3'-oligo-T-primer was replaced by T7-promoter-containing-oligo-T-primer (DNA-synthesis, Russia); 2. cDNA was complemented to ds-cDNA by 15-cycles PCR amplification; 3. ds-cDNA (2 ug) was transcribed by T7 RNA-polimerase (Thermo Scientific, EU). Biotin-labeled RNA was obtained using biotinylated UTP (DNA-synthesis, Russia) by substitution of a half of its unlabeled counterpart in reaction mix.

extract_protocol: Total RNA was isolated by magnetic beads-containg kit (Magnosorb kit, Russia) followed by phenol-chloroform purification

tag: Stage

value: healthy donor

tag: gender

value: female

tag: age

value: peripheral blood leukocytes


title: H3_E50K_RGC_D10_p31_S14

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

country: USA

institute: INDIANA UNIVERSITY

data_processing:
Data is mapping to human genome GRCh38 using STAR software
counts data are extract using featureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: counts data

source_name: OPTN (E50K) iPSC-dervied RGC

growth_protocol: hPSCS were differentiated into retinal organoids. Retinal organoids were then dissoicated and RGCs were purified, and then plated on coverslips for 10 days. RNA was collected directly from the coverslips.

extract_protocol:
The RGCs were lysed and total RNA was extracted  with the PicoPure RNA isolation kit.
RNA libraries were prepared for sequencing using standard protocols

value: human pluripotent stem cell-derived retinal ganglion cells

tag: genotype/variation

value: E50K mutation in the Optineurin (OPTN) gene

tag: time point

value: 45 days of differentiation with additional 10 days after RGCs purification


title: D16_3: donor_16_rep 3


title: D17_3: donor_17_rep 3


title: CLOCK defecient hMSCs rep 3 [ChIP-Seq]

description:
H3K9me3 ChIP-seq of CLOCK deficient hMSCs.
H3K9me3_CLOCK.bin_10.bw


title: D16_1: donor_16_rep 1


title: D15_3: donor_15_rep 3

value: male


title: WT hMSCs rep 3 [ChIP-Seq]


title: CLOCK defecient hMSCs rep 2 [ChIP-Seq]


title: CLOCK defecient hMSCs rep 1 [ChIP-Seq]


title: SW480 Clone2

description:
Control
long non-coding RNAs
SAMPLE 2

source_name: SW480 Clone2


title: WT hMSCs rep 2 [ChIP-Seq]


title: D17_1: donor_17_rep 1


title: WT hMSCs rep 3 [ATAC-Seq]

description:
ATAC sequencing of WT hMSCs.
ATAC_WT.bin_10.bw


title: D15_1: donor_15_rep 1


title: D16_2: donor_16_rep 2


title: D14_3: donor_14_rep 3


title: D15_2: donor_15_rep 2


title: WT hMSCs rep 2 [ATAC-Seq]


title: WT hMSCs rep 1 [ATAC-Seq]


title: CLOCK defecient hMSCs rep 3 [ATAC-Seq]

description:
ATAC sequencing of CLOCK deficient hMSCs.
ATAC_CLOCK.bin_10.bw


title: CLOCK defecient hMSCs rep 2 [ATAC-Seq]


title: CRISPRa_U937_2_NS

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

data_processing:
Library strategy: CRISPR guide-seq
For CRISPRi/a analysis, reads covering the guide sequences from each bin were aligned to the designed guide sequences using Bowtie2 (2.2.1; default settings), and the total number of each guide observed in each bin counted.
Guide-level and element-level effects were estimated using MAUDE (https://github.com/Carldeboer/MAUDE/), where elements corresponded to either targeted SNPs (CRIPSRa), or targeted open chromatin regions (CRISPRi).
For an element to be considered significantly regulating TNFAIP3, we required that both replicates’ Benjamini-Hochberg FDRs were less than sqrt(0.1) (i.e. combined FDR<0.1, and both replicates close to significant independently) and for which the direction of expression change was identical.  In cases where there were more than two replicates, we included only the two replicates for which the TNFAIP3 promoter positive control guides showed the strongest effect.
Supplementary_files_format_and_content: Tab-delimited text containing guide IDs/sequences, and count matrices for each sample.

growth_protocol: BJAB, Jurkat, U937, THP-1, and GM12878 cell lines were cultured using RPMI 1640 (ThermoFisher, 21870092) containing 10% fetal bovine serum (FBS, VWR, 97068-091; 20% for GM12878) with 1% Penn/strep (VWR, 45000-652), 1% L-Glutamine (ThermoFisher, 25030081), and 1% HEPES (Sigma, H0887-100ML). Cells were maintained at a culture density between 100K-1M cells/mL.

extract_protocol:
Cells expressing CRISPRi or CRISPRa constructs along with sgRNA libraries were sorted into six 10% bins, sorting on the extremes of expression (30% on either the low or high portion of the expression distribution, each divided into three contiguous bins each comprised of approximately 10% of the overall distribution). For each experiment and cell type, between 300K and 1M cells were sorted per bin. Genomic DNA for each sample was then reverse-crosslinked using ChIP Lysis Buffer (1% SDS, 0.01M EDTA, 0.05M Tris HCl pH 7.5). Briefly, sorted cells were spun at 800g for 10 min at 4C, the supernatant was aspirated, and the cells were resuspended in 50 μL of ChIP Lysis Buffer, and incubated at 65C for 10 min. The samples were then cooled to 37C and 2 μL of RNase Cocktail (ThermoFisher, AM2286) was added to each sample and the sample was mixed well by pipetting, followed by incubation at 37C for 30 min. 10μL of Proteinase K (NEB, P8107S) was added to each sample and the sample was mixed well by pipetting, followed by incubation at 37C for 2 hours and then 95C for 20 min. gDNA was extracted using Agencourt XP beads at 0.7X following the manufacturers protocol, and the sample was eluted at 100 μL.
Libraries were prepared by PCR of each sample, splitting each in to 4 50 μL reactions (25 μL NEB Next Master Mix, 2.5 μL barcoded sequencing forward and reverse primers (Ext. Data Table 10), 11.5 μL gDNA, and 11.5 μL ddH2O; program: 98C for 30s, 25 cycles of 98C for 15s, 62C for 15s, 72C for 16s, then 72C for 2 min. The libraries were then gel purified using a 2% gel (expected band size of 206 bp). Samples were sequenced aiming to get >1,000,000 reads per bin, on either an Illumina HiSeq 2500 or MiSeq using a custom sequencing and index primers for CRISPRi and CRISPRa (Ext. Data Table 10).

treatment_protocol: Jurkat T cells were stimulated with 2.5 ug/mL of anti-CD3 (Biolegend, 317304) and 10 ng/mL of PMA (Sigma, P1585-1MG) for 1 hour prior to harvesting for CRISPRi. BJAB and GM12878 B cells were stimulated with 2.5 ug/ml of anti-IgM and 2 ug/ml anti-CD40 for 2 hours for CRISPRi. THP-1 and U937 monocytes were stimulated with 100 ng/mL LPS for 2 hours for CRISPRi. CRISPRa samples were unstimulated.

tag: screen type

value: CRISPRa

tag: replicate id

tag: sorting bin

value: NS


title: CRISPRa_U937_2_E

value: E


title: D14_2: donor_14_rep 2


title: D14_1: donor_14_rep 1


title: D13_3: donor_13_rep 3


title: CRISPRa_U937_2_C

value: C


title: CRISPRa_U937_2_D

value: D


title: CLOCK defecient hMSCs rep 1 [ATAC-Seq]

value: Mesenchymal stem cell


title: CRISPRa_U937_2_B

value: B


title: D13_2: donor_13_rep 2


title: CUTLL1-shAURKB-3

city: Wuhan

first: jue

last: jiang

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province

department: Medical Research Institute

institute: Wuhan University

data_processing:
The main steps of applying Seqtk for filtering are as follows:1、Remove the sequence of joints contained in reads；2、Remove bases with 3 'end mass Q less than 20, that is, the base error rate is less than 0.01，among,Q=-10logerror_ratio；3、Remove reads with length less than 25；4、Remove ribosome RNA reads of the species。
Spliced mapping algorithm of Hisat2 (version:2.0.4) was applied to Genome mapping of preprocessed reads，Take default parameters. The alignment result generated by Mapping is BAM file
Application Stringtie (version: 1.3.0)in Hisat2 than after each gene Fragments could count to count, and then use TMM (trimmed mean of M values) normalization method, finally calculated using perl script FPKM value of each gene.
In order to make gene expression levels between different genes and samples comparable, reads were transformed into FPKM (Fragments Per Kilobase of exon model Per Million mapped reads) to standardize gene expression
EdgeR was used for gene analysis of differences between samples, and multiple hypothesis test and correction were carried out after p-value was obtained. The threshold value of p-value was determined by controlling FDR (False Discovery Rate), and the p-value after correction was q-value.Meanwhile, we calculate Fold-change according to FPKM.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: FPKM

source_name: CUTLL1 Cell Line

growth_protocol: CUTLL1 cells were grown in complete RPMI-1640 (Hyclone) supplemented with 10% fetal bovine serum (FBS, Hyclone), 1% penicillin/ streptomycin (Hyclone), 1% non-essential amino acids (Gibco), 2mM L-glutamine (Sigma), 1 mM sodium pyruvate (Sigma), and 55μM β-mercaptoethanol (Sigma).

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CUTLL1 cells were infected with control shRNA, AURKB shRNA respectively, and selected with puromycin for 48 hours.

tag: treatment

value: transfected with AURKB shRNA


title: CRISPRa_U937_1_NS


title: D13_1: donor_13_rep 1


title: CRISPRa_U937_2_A

value: A


title: D12_2: donor_12_rep 2


title: CRISPRa_U937_1_F

value: F


title: CRISPRa_U937_1_E


title: CRISPRa_U937_1_D


title: CUTLL1-shAURKB-2


title: CUTLL1-shAURKB-1


title: D12_1: donor_12_rep 1

value: healthy donor


title: CUTLL1-shGFP-3

value: transfected with control shRNA


title: CRISPRa_U937_1_B


title: CRISPRa_U937_2_F


title: D12_3: donor_12_rep 3

value: peripheral blood leukocytes


title: CRISPRa_U937_1_A


title: CUTLL1-shGFP-2


title: CRISPRa_THP1_2_NS


title: WT hMSCs  [ChIP-Seq]

description:
Input file corresponding to H3K9me4 ChIP-seq data of WT hMSCs.
H3K9me3_WT.bin_10.bw

value: WT hMSCs


title: CRISPRa_THP1_2_F


title: CRISPRa_THP1_2_E


title: CUTLL1-shGFP-1


title: CRISPRa_THP1_2_D


title: D11_2: donor_11_rep 2


title: D11_3: donor_11_rep 3


title: TNF-a rep2

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: nucleus pulposus cells

growth_protocol: Normal nucleus pulposus tissue were dissected during the surgery, all tissues were obtained with written informed consent signed by the donors voluntarily for research.nucleus pulposus tissue were further digested using Type II & IV collagenase for 4h and cultured in DMEM supplemented with 20% fetal bovine serum, and cells of passage 4 were used for the experiments.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Each sample were treated with IL-1b, TNF-a, IL-1b+CHI3L1 (100ug/ml) or TNF-a+CHI3L1 (100ug/ml) for 48h according to the label.

value: normal nucleus pulposus

value: Passage 4

tag: Sex

tag: agent

value: TNF-a


title: D11_1: donor_11_rep 1

value: male


title: CRISPRa_THP1_2_C

value: CRISPRa


title: CRISPRa_THP1_2_B


title: TNF-a rep1


title: CRISPRa_THP1_2_A


title: D10_3: donor_10_rep 3


title: CRISPRa_U937_1_C


title: CRISPRa_THP1_1_NS

value: NS


title: TNF-a+CHI3L1 rep2


title: CRISPRa_THP1_1_F


title: TNF-a+CHI3L1 rep1


title: D10_2: donor_10_rep 2


title: D10_1: donor_10_rep 1


title: CRISPRa_THP1_1_E

value: E


title: IL-1b rep2


title: D9_3: donor_9_rep 3


title: CRISPRa_THP1_1_C

value: C


title: D9_2: donor_9_rep 2


title: CRISPRa_THP1_1_B


title: IL-1b rep1


title: CRISPRa_Jurkat_2_NS

source_name: Jurkat

value: Jurkat


title: CRISPRa_Jurkat_2_F


title: CRISPRa_THP1_1_A


title: IL-1b+CHI3L1 rep2


title: CRISPRa_Jurkat_2_E


title: CRISPRa_Jurkat_2_D

value: D


title: IL-1b+CHI3L1 rep1


title: CRISPRa_Jurkat_2_C


title: CRISPRa_Jurkat_2_B

value: B


title: CRISPRa_Jurkat_2_A

value: A


title: CRISPRa_Jurkat_1_NS


title: CRISPRa_THP1_1_D


title: D8_1: donor_8_rep 1


title: CRISPRa_Jurkat_1_F

value: F


title: CRISPRa_Jurkat_1_E


title: D7_3: donor_7_rep 3

value: healthy donor


title: CRISPRa_Jurkat_1_D


title: D8_2: donor_8_rep 2


title: CRISPRa_Jurkat_1_B


title: Time 40_Apicoplast_Rep 4

city: Baltimore

first: Anne

middle: E.

last: Jedlicka

state: MD

address: 615 N. Wolfe street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University, School of Public Health

description: Gene Expression Data

hyb_protocol: The eight time course samples were hybridized (along with the manufacturer’s RNA spike-in controls) according to standard protocol to the 8 sectors of an Agilent 8x15K platform microarray (AMADID 037237) with separate microarray slides used for each biological replicate (in quadruplicate for each condition).

scan_protocol: Arrays were scanned with the Agilent G2600D SureScan microarray scanner using scan protocol AgilentHD_GX_1color. Agilent’s Feature Extraction Software was used to assign grids, provide raw image files per array, and generate QC metric reports from the microarray scan data.

data_processing: Txt files from Agilent’s Feature Extraction Software were transferred to Partek Genomics Suite software (v7.0). Within Partek, the gProcessedSignal was imported and the intensity values were normalized using Quantile Normalization and Log Tranformation Base 2.0 after import.

organism: Plasmodium falciparum

source_name: Apicoplast negative PfMev parasites, Time 40, Rep 4

label_protocol: From 100 ng of total RNA, Cyanine-3 labeled cRNA was prepared using the Low Input Quick Amp Labeling Kit One-Color (Agilent).

growth_protocol: Blood-stage P. falciparum parasites were cultured in human erythrocytes at 2% hematocrit in CMA (Complete Medium with Albumax) containing RPMI 1640 medium with L-glutamine (USBiological Life Sciences), supplemented with 20mM HEPES, 0.2% sodium bicarbonate, 12.5μg/ml hypoxanthine, 0.5μM R-lipoic acid, 5g/L Albumax II (Life Technologies) and 25μg/mL gentamicin. Cultures were maintained in 25cm2 gassed flasks (94% N2, 3% O2, 3% CO2) and incubated at 37°C.

extract_protocol: For each data point, RNA was extracted from 50 µL of packed RBC culture with Trizol Reagent and the PureLink Mini Kit (Invitrogen/Thermo Fisher Scientific). 1ml Trizol was added to each sample, followed by high-speed disruption in tubes containing Lysing Matrix D (MP Biomedical) in a FastPrep 120 Instrument at speed 6 for 20 seconds. Homogenates were subsequently processed according to the PureLink Mini Kit manufacturer’s (Invitrogen/Thermo Fisher Scientific) protocol, including on-column DNase treatment.

treatment_protocol: Genetically engineered Plasmodium falciparum parasites (PfMev) were treated with azithromycin to disrupt the apicoplast. These apicoplast negative PfMev parasites were cultured as described in in the paper, at 2% hematocrit and supplemented with 50μM mevalonate.

value: Blood-stage Apicoplast negative Pfmev NF54attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit and  supplemented with 50μM mevalonate

tag: time

value: Time 40

value: Apicoplast

tag: slide id (array batch)

tag: replicate

value: Rep 4


title: D9_1: donor_9_rep 1

tag: tissue

value: peripheral blood leukocytes


title: D7_2: donor_7_rep 2


title: CRISPRa_Jurkat_1_C

tag: cell type


title: Time 48_Apicoplast_Rep 4

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 48, Rep 4

value: Time 48


title: CRISPRa_Jurkat_1_A


title: D8_3: donor_8_rep 3

value: male


title: CRISPRa_BJAB_2_D

source_name: BJAB

value: CRISPRa

value: BJAB


title: CRISPRa_BJAB_2_F


title: CRISPRa_BJAB_2_E

value: E


title: D6_1: donor_6_rep_1


title: D6_2: donor_6_rep_2


title: D7_1: donor_7_rep 1


title: CRISPRa_BJAB_2_NS

value: NS


title: CRISPRa_BJAB_2_C

value: C


title: Time 16_Apicoplast_Rep 4

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 16, Rep 4

value: Time 16


title: CRISPRa_BJAB_2_B

value: B


title: CRISPRa_BJAB_2_A

value: A


title: Time 24_Apicoplast_Rep 4

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 24, Rep 4

value: Time 24


title: D5_3: donor_5_rep 3

value: healthy donor


title: CRISPRa_BJAB_1_NS


title: CRISPRa_BJAB_1_F

value: F


title: D5_2: donor_5_rep 2


title: D5_1: donor_5_rep 1


title: Time 32_Apicoplast_Rep 4

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 32, Rep 4

value: Blood-stage Apicoplast negative Pfmev NF54attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit and  supplemented with 50μM mevalonate

value: Time 32


title: Time 48_Apicoplast_Rep 3

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 48, Rep 3

value: Apicoplast

value: Rep 3


title: Time 40_Apicoplast_Rep 3

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 40, Rep 3

value: Time 40


title: CRISPRa_BJAB_1_D

value: D


title: CRISPRa_BJAB_1_C

value: CRISPRa


title: CRISPRa_BJAB_1_E

value: BJAB


title: Time 32_Apicoplast_Rep 3

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 32, Rep 3


title: CRISPRa_BJAB_1_B


title: D4_3: donor_4_rep 3

value: female

value: peripheral blood leukocytes


title: CRISPRa_BJAB_1_A


title: Time 08_Apicoplast_Rep 4

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 08, Rep 4

value: Time 08

value: Rep 4


title: D4_2: donor_4_rep 2


title: BKO-3

city: Augusta

first: Weiqin

last: Chen

state: GA

address: 1462 Laney Walker Blvd

department: Physiology

institute: Augusta University

description:
Sample name:
WT3

data_processing:
The Illumina sequencing tool Casava version 1.8 was employed for converting raw images to base calls. generating sequence reads, and de-multiplexing the reads into the corresponding index-attached files.
Tophat 2.0.12:tophat was used for accurate alignment of transcriptomes of RNA-seq reads against library-type fr-firststrand -G mm.Ensembl-NCBIM37.igenes.gtf
Cufflinks 2.2.1 was used to assemble transcripts, estimate their abundances, and test for differential expression and regulation in RNA-Seq samples
Genome_build: Ensembl-NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: brown adipose tissue

extract_protocol:
Invitrogen Trizol
illumina TruSeq RNA Library Prep Kit v2

value: brown adipose

tag: strain

value: 10 week old

value: male


title: D4_1: donor_4_rep 1

source_name: peripheral blood leukocytes

tag: Stage

value: healthy donor


title: BKO-1

description:
Sample name:
WT1


title: Ctrl-3

description:
Sample name:
MT3


title: Time 24_Apicoplast_Rep 3

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 24, Rep 3

value: Time 24


title: Time 16_Apicoplast_Rep 3

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 16, Rep 3

value: Blood-stage Apicoplast negative Pfmev NF54attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit and  supplemented with 50μM mevalonate

value: Time 16


title: Ctrl-2

description:
Sample name:
MT2


title: Ctrl-1

description:
Sample name:
MT1


title: D3_2: donor_3_rep 2

tag: gender


title: D3_3: donor_3_rep 3

tag: age


title: Time 08_Apicoplast_Rep 3

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 08, Rep 3

value: Apicoplast


title: norUDCA-diet Mouse liver RNAseq [WT20]

city: Atlanta

first: Paul

last: Dawson

address: 1760 Haygood Drive

department: Division of Pediatric GI/Hepatology

institute: Emory University

data_processing:
Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Data Filtering was performed to remove reads containing adaptors, N>10% or the Qscore of over 50% bases of the read is <=5
After data cleaning, clean reads were mapped to the reference transcriptome by STAR software to make the junction reads be positioned precisely
Gene expression levels can be calculated by the number of mapped reads, more specifically, the abundance of transcripts (count of sequencing) that mapped to genome or exon.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package. And the resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. (Kij ～ NB(μij,σij2))
Supplementary_files_format_and_content: Readcounts of genes in excel file.

source_name: norUDCA-diet Mouse liver RNAseq

extract_protocol:
Total RNA was extracted from frozen tissue using TRIzolreagent (Invitrogen, Carlsbad, CA)
Libraries were generated using the NEBNext Library method for the Illumina system following the manufacturer’s instructions

treatment_protocol: Male C57Bl/6J mice at age of 13 weeks were fed with Chow or 0.5%norUDCA containing diet for one week. Livers were harvested and frozen in liquid N2.

tag: strain and sex

value: 13 wks

tag: diet

value: norUDCA-diet

value: liver


title: norUDCA-diet Mouse liver RNAseq [WT13]


title: norUDCA-diet Mouse liver RNAseq [WT10]


title: D3_1: donor_3_rep 1


title: norUDCA-diet Mouse liver RNAseq [WT11]


title: Time 48_Apicoplast_Rep 2

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 48, Rep 2

value: Time 48

value: Rep 2


title: BKO-2

description:
Sample name:
WT2


title: norUDCA-diet Mouse liver RNAseq [WT9]


title: Chow-diet Mouse liver RNAseq [WT17]

source_name: Chow-diet Mouse liver RNAseq

value: Chow-diet


title: D2_3: donor_2_rep 3

value: peripheral blood leukocytes


title: D2_2: donor_2_rep 2


title: Chow-diet Mouse liver RNAseq [WT16]


title: D2_1: donor_2_rep 1


title: Time 0_Apicoplast_Rep 3

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 0, Rep 3

value: Time 0

value: Rep 3


title: Time 32_Apicoplast_Rep 2

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 32, Rep 2

value: Time 32


title: Time 40_Apicoplast_Rep 2

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 40, Rep 2

value: Time 40


title: Time 24_Apicoplast_Rep 2

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 24, Rep 2


title: Chow-diet Mouse liver RNAseq [WT8]

value: male


title: Chow-diet Mouse liver RNAseq [WT7]


title: D1_3: donor_1_rep 3

value: healthy donor


title: D1_2: donor_1_rep 2


title: Chow-diet Mouse liver RNAseq [WT3]


title: norUDCA-diet Mouse liver RNAseq [WT12]


title: 12_CV_F3

first: Bejan

last: Saeedi

address: 615 Michaels St

department: Pathology

data_processing:
fastq files were aligned to mouse reference genome GRCm38
Transcript abundance was estimated using htseq-count v0.6.1p1
Differential expression analyses were performed using DESeq2.
Genome_build: Mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million values for each Sample …

source_name: Liver

growth_protocol: Mice were maintained in sterile isolators until weaning (21 days).

extract_protocol:
RNA was isolated from snap frozen liver tissues using the Qiagen RNeasy mini kit (Qiagen) and assessed for integrity and quantity using an Agilent Bioanalyzer (Agilent Technologies) and a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific).
Libraries were prepared using the Illumina TruSeq mRNA stranded kit as per the manufacturer’s instructions.

treatment_protocol: Mice were either maintained in sterile isolators or moved out of the isolators and put in cages containing dirty bedding from elsewhere in the animal facility. Mice were sacrificed at 6 weeks of age (3 weeks of conventionalization).

tag: background strain

value: Conventionalized

value: Female


title: D1_1: donor_1_rep 1


title: 11_CV_F2


title: Time 08_Apicoplast_Rep 2

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 08, Rep 2

value: Blood-stage Apicoplast negative Pfmev NF54attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit and  supplemented with 50μM mevalonate

value: Time 08


title: Time 0_Apicoplast_Rep 2

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 0, Rep 2

value: Apicoplast


title: 9_CV_M3

value: Male


title: P6_AC_3: patient_6_acute_rep 3

value: acute EBV infection

value: female


title: Time 16_Apicoplast_Rep 2

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 16, Rep 2

value: Time 16

value: Rep 2


title: 7_CV_M1


title: P6_AC_2: patient_6_acute_rep 2

value: peripheral blood leukocytes


title: Time 48_Apicoplast_Rep 1

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 48, Rep 1

value: Time 48

value: Rep 1


title: Time 40_Apicoplast_Rep 1

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 40, Rep 1


title: 8_CV_M2


title: P6_AC_1: patient_6_acute_rep 1

source_name: peripheral blood leukocytes


title: 5_GF_F2

value: Germ-free


title: Time 32_Apicoplast_Rep 1

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 32, Rep 1

value: Time 32


title: 6_GF_F3


title: 4_GF_F1


title: 3_GF_M3


title: 2_GF_M2


title: Chow-diet Mouse liver RNAseq [WT2]

value: male

value: 13 wks

value: Chow-diet

value: liver


title: P5_REC_3: patient_5_recovery_rep 3

value: after recovery


title: P5_REC_2: patient_5_recovery_rep 2


title: 1_GF_M1


title: input_library_3.4E6_barcode_allele_matching

description: enhancer_barcode_association_3.4E6_2.map.gz

data_processing:
A bowtie index of the ordered probe sequences and 16Ns for the barcode was created and the long reads for mapping barcodes to enhancers aligned to this index using Bowtie2. Associated barcodes were extracted and classified into those that map uniquely to a specific error-free probe, and those that do not (probe_barcode_association_3.4E6_2.map.gz).
MPRA RNA output and DNA input sequencing reads were mapped to the known tag sequences using a custom python script (quantifyRNATags.py), allowing for up to four mismatches within the constant region (the common sequence before the tag sequence) and no mismatches within the tag sequence.
The barcode counts were input, and tags having fewer than 30 reads in the input (DNA) or 4 reads in the output (RNA) were excluded from subsequent analysis.
The log(DNA/RNA) ratio (“expression”) was calculated using raw counts, scaled so that the median expression is 0, and the expression levels G+C-content normalized such that the mean expression for every %G+C was 0.
Finally, to eliminate instances where the tag sequence modifies the apparent expression level, any tags containing any one of eight blackballed 5-mer DNA sequences were excluded. Blackballed 5-mers were defined as those for which the absolute value of the average expression level of all tags containing that 5-mer was greater than 0.15.
SNPs were tested for allele-specific reporter activity by a two-sided Student’s t-test, comparing the normalized log(RNA/DNA) expression values for the tags for allele A compared to the tags for allele B. Only SNPs for which we had at least 80 good tags between the two alleles were tested. P-values were corrected for multiple hypothesis testing by Benjamini-Hochberg FDR correction. Only SNPs that had an FDR<0.1 for at least two of the replicates and where the direction of allele- specific reporter activity was consistent between all replicates were considered to be significant.
Genome_build: hg19
Supplementary_files_format_and_content: gzipped tab delimited or fasta; barcodes for each element, enhancer sequences

organism: unidentified plasmid

source_name: plasmid

growth_protocol: BJAB, Jurkat, U937, and GM12878 cell lines were cultured using RPMI 1640 (ThermoFisher, 21870092) containing 10% fetal bovine serum (FBS, VWR, 97068-091; 20% for GM12878) with 1% Penn/strep (VWR, 45000-652), 1% L-Glutamine (ThermoFisher, 25030081), and 1% HEPES (Sigma, H0887-100ML). Cells were maintained at a culture density between 100K-1M cells/mL.

extract_protocol:
Total RNA was extracted from cells using Qiagen Maxi RNeasy (Qiagen, 75162) following the manufacturer’s protocol including the on-column DNase digestion. A second DNase treatment was performed on the purified RNA using 5 μL of Turbo DNase (Life Technologies, AM2238) with buffer, in 750 μL of total volume for 1 hour at 37°C. The digestion was stopped with the addition of 7.5 μL 10% SDS and 75 μL of 0.5M EDTA followed by a 5 minute incubation at 70°C. The total reaction was then used for pulldown of GFP mRNA. Water was added to the DNase digested RNA to bring the total volume to 898 μL to which 900 μL of 20X SSC (Life Technologies, 15557-044), 1800 μL of Formamide (Life Technologies, AM9342) and 2 μL of 100 uM biotin-labeled GFP probe (GFP_BiotinCapture_1-3, IDT, Ext. Data Table 10) were added and incubated for 2.5 hours at 65°C. Biotin probes were captured using 400 μL of pre- washed Streptavidin beads (Life Technologies, 65001) eluted in 500 μL of 20X SSC. The hybridized RNA/probe bead mixture was agitated on a nutator at room temperature for 15 minutes. Beads were captured by magnet and washed once with 1x SSC and twice with 0.1x SSC. Elution of RNA was performed by the addition of 25 μL water and heating of the water/bead mixture for 2 minutes at 70°C followed by immediate collection of eluent on a magnet. A second elution was performed by incubating the beads with an additional 25 μL of water at 80°C. A final DNase treatment was performed in 50 μL total volume using 1 μL of Turbo DNase with addition of the buffer incubated for 60 minutes at 37°C followed by inactivation with 1 μL of 10% SDS and purification using RNA clean SPRI beads (Beckman Coulter, A63987).
First-strand cDNA was synthesized from half of the DNase-treated GFP mRNA with SuperScript III and a primer specific to the 3’ UTR (MPRA_v3_Amp2Sc_R) using the manufacturer’s recommended protocol, modifying the total reaction volume to 40 μL and performing the elongation step at 47°C for 80 minutes. Single-stranded cDNA was purified by SPRI and eluted in 30 μL EB.  To minimize amplification bias during the creation of cDNA tag sequencing libraries, samples were amplified by qPCR to estimate relative concentrations of GFP cDNA using 1 μL of sample in a 10 μL PCR reaction containing 5 μL Q5 NEBNext master mix, 1.7 μL Sybr green I diluted 1:10,000 (Life Technologies, S-7567) and 0.5 uM of TruSeq_Universal_Adapter and MPRA_Illumina_GFP_F primers (Ext. Data Table 10). Samples were amplified with the following qPCR conditions: 95°C for 20 seconds, 40 cycles (95°C for 20 sec, 65°C for 20 sec, 72°C for 30 sec), 72°C for 2 min. The number of cycles for sample amplification was 1-n (the number of cycles it took for each sample to pass the threshold) from the qPCR. To add Illumina sequencing adapters, 10  uL of cDNA samples and mpra:pTNFAIP3:gfp plasmid control (diluted to the qPCR cycle range of the samples) were amplified using the reaction conditions from the qPCR scaled to 50 uL, excluding Sybrgreen I. Amplified cDNA was SPRI purified and eluted in 40 μL of EB. Individual sequencing barcodes were added to each sample by amplifying the entire 40 μL elution in a 100 μL Q5 NEBNext reaction with 0.5 uM of TruSeq_Universal_Adapter primer and a reverse primer containing a unique 8 bp index (Illumina_Multiplex, Ext. Data Table 10) for sample demultiplexing post-sequencing. Samples were amplified at 95°C for 20 seconds, 6 cycles (95°C for 20 sec, 64°C for 30 sec, 72°C for 30 sec), 72°C for 2 minutes. Indexed libraries were SPRI purified and pooled according to molar estimates from Agilent TapeStation quantifications. Samples were sequenced using 1x30 bp chemistry on an Illumina HiSeq 2500 or NextSeq.   To determine oligo/barcode combinations within the MPRA pool, Illumina libraries were prepared from the mpra∆orf plasmid library by performing 4 separate amplifications with 200 ng of plasmid in a 100 μL Q5 NEBNext PCR reaction containing 0.5 uM of TruSeq_Universal_Adapter and MPRA_v3_TruSeq_Amp2Sa_F primers with the following conditions: 95°C for 20 sec, 6 cycles (95°C for 20 sec, 62°C for 15 sec, 72°C for 30 sec), 72°C for 2 minutes. Amplified material was SPRI purified using a 0.6x bead/sample ratio and eluted with 30 μL of EB. Sequencing indexes were then attached using 20 μL of the eluted product and the same reaction conditions as for the tag-seq protocol, except the number of enrichment cycles was lowered to 5. Samples were molar pooled and sequenced using 2x150 bp chemistry on Illumina HiSeq 2500 and NextSeq.
MPRA library preparation

treatment_protocol: Jurkat T cells were stimulated with 2.5 ug/mL of anti-CD3 (Biolegend, 317304) and 10 ng/mL of PMA (Sigma, P1585-1MG) for 1 hour prior to harvesting. BJAB and GM12878 B cells were stimulated with 2.5 ug/ml of anti-IgM and 2 ug/ml anti-CD40 for 2 hours. U937 monocytes were stimulated with 100 ng/mL LPS for 2 hours.

tag: stim condition

tag: cell line

tag: vector delivery


title: 10_CV_F1

tag: treatment

value: Conventionalized

tag: Sex

value: Female


title: Time 16_Apicoplast_Rep 1

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 16, Rep 1

value: Blood-stage Apicoplast negative Pfmev NF54attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit and  supplemented with 50μM mevalonate

tag: time

value: Apicoplast


title: P5_REC_1: patient_5_recovery_rep 1

value: female


title: WT hMSCs rep 3 [DamID-seq] EMD

description:
DamID sequencing of WT hMSCs.
WT_log2_nom_Dam_EMD_vs_Dam.bin_10.bw

data_processing:
Library strategy: DamID-seq
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2 or histat2 software.
Genome_build: hg19 for Homo sapiens and mm10 for Mus musculus data.
Supplementary_files_format_and_content: Txt file of read count for RNA-seq. bw file fof RPKM normalized read cout for each 10 bp bin size for others sequencing data.

source_name: Mesenchymal stem cell

value: Mesenchymal stem cell

tag: genotype

value: WT hMSCs

tag: passage


title: input_barcode_abundance_sequencing

tag: replicate


title: WT hMSCs rep 2 [DamID-seq] EMD

tag: cell type


title: P5_AC_3: patient_5_acute_rep 3

value: acute EBV infection

tag: tissue

value: peripheral blood leukocytes


title: WT hMSCs rep 1 [DamID-seq] EMD


title: P5_AC_2: patient_5_acute_rep 2

tag: Stage


title: CLOCK defecient hMSCs rep 3 [DamID-seq] EMD

description:
DamID sequencing of CLOCK deficient hMSCs.
CLOCK_log2_nom_Dam_EMD_vs_Dam.bin_10.bw

value: CLOCK defecient hMSCs


title: Time 48_Control_Rep 4

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 48, Rep 4

value: Blood-stage Nf54 attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit

value: Time 48

value: Control

tag: slide id (array batch)

value: Rep 4


title: Time 40_Control_Rep 4

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 40, Rep 4

value: Time 40


title: CLOCK defecient hMSCs rep 2 [DamID-seq] EMD


title: CLOCK defecient hMSCs rep 1 [DamID-seq] EMD


title: WT hMSCs rep 3 [DamID-seq]


title: Time 0_Apicoplast_Rep 1

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 0, Rep 1

value: Time 0

value: Rep 1


title: Time 32_Control_Rep 4

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 32, Rep 4

value: Time 32


title: WT hMSCs rep 2 [DamID-seq]


title: P4_REC_3: patient_4_recovery_rep 3

value: after recovery

tag: gender

value: male

tag: age


title: P5_AC_1: patient_5_acute_rep 1


title: Time 08_Apicoplast_Rep 1

description: Gene Expression Data

source_name: Apicoplast negative PfMev parasites, Time 08, Rep 1

value: Blood-stage Apicoplast negative Pfmev NF54attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit and  supplemented with 50μM mevalonate

value: Time 08

value: Apicoplast


title: WT hMSCs rep 1 [DamID-seq]

value: Mesenchymal stem cell

value: WT hMSCs


title: CLOCK defecient hMSCs rep 3 [DamID-seq]


title: CLOCK defecient hMSCs rep 2 [DamID-seq]


title: P4_REC_2: patient_4_recovery_rep 2

value: peripheral blood leukocytes


title: P4_REC_1: patient_4_recovery_rep 1


title: P4_AC_3: patient_4_acute_rep 3

value: acute EBV infection


title: P4_AC_2: patient_4_acute_rep 2


title: CLOCK defecient hMSCs rep 1 [DamID-seq]

value: CLOCK defecient hMSCs


title: Time 16_Control_Rep 4

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 16, Rep 4

value: Blood-stage Nf54 attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit

value: Time 16


title: Time 0_Control_Rep 4

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 0, Rep 4

value: Control

value: Rep 4


title: Time 08_Control_Rep 4

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 08, Rep 4


title: transfection_Jurkat_3_unstim

source_name: T lymphocyte from acute T cell leukemia

value: Jurkat

value: transfection


title: P3_REC_2: patient_3_recovery_rep 2


title: P4_AC_1: patient_4_acute_rep 1


title: transfection_Jurkat_3_stim

value: 2.5ug/ml anti-CD3 + 50 ng/ml PMA 1 hour


title: Time 48_Control_Rep 3

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 48, Rep 3

value: Time 48

value: Rep 3


title: Time 24_Control_Rep 4

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 24, Rep 4

value: Time 24


title: Time 32_Control_Rep 3

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 32, Rep 3

value: Time 32


title: transfection_Jurkat_2_unstim


title: Time 40_Control_Rep 3

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 40, Rep 3

value: Time 40


title: P3_REC_1: patient_3_recovery_rep 1

source_name: peripheral blood leukocytes

value: after recovery

value: male


title: P3_AC_3: patient_3_acute_rep 3

value: peripheral blood leukocytes


title: Time 16_Control_Rep 3

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 16, Rep 3


title: transfection_Jurkat_1_unstim


title: P3_REC_3: patient_3_recovery_rep 3


title: Time 0_Control_Rep 3

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 0, Rep 3

value: Time 0


title: U87-NC_T1-3, biological rep3

city: Tianjin

first: Rong

last: Fan

address: 1st Huizhihuan Road

institute: Logistic University of Chinese People’s Armed Police Force

description: Gene expression data from U87-NC cells

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 .

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: U87-PCGF1-shRNA and U87-NC cell lines were cultured in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000.

treatment_protocol: U87 Cells were transfected with PCGF1-shRNA and NC lentivirus.

value: human glioma cells

tag: genotype/variation

value: negative control


title: U87-NC_T1-2, biological rep2

description: Gene expression data from U87-NC cells


title: Time 24_Control_Rep 3

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 24, Rep 3

value: Blood-stage Nf54 attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit


title: P3_AC_2: patient_3_acute_rep 2

value: acute EBV infection


title: transfection_Jurkat_1_stim


title: transfection_Jurkat_2_stim


title: P2_REC_3: patient_2_recovery_rep 3


title: Time 40_Control_Rep 2

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 40, Rep 2

value: Control

value: Rep 2


title: joints of aged mice injected with lentivirus expressing Luc  rep 2 [RNA-Seq]

description: RNA-seq of joints of aged mice injected with lentivirus expressing Luc.

source_name: Joints

value: Joints


title: P2_REC_1: patient_2_recovery_rep 1


title: P2_REC_2: patient_2_recovery_rep 2


title: Time 32_Control_Rep 2

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 32, Rep 2


title: Time 08_Control_Rep 3

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 08, Rep 3

value: Time 08


title: Time 24_Control_Rep 2

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 24, Rep 2


title: P2_AC_3: patient_2_acute_rep 3


title: Time 16_Control_Rep 2

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 16, Rep 2

value: Time 16


title: Time 08_Control_Rep 2

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 08, Rep 2


title: joints of aged mice injected with lentivirus expressing Luc  rep 1 [RNA-Seq]


title: joints of aged mice injected with lentivirus expressing CLOCK  rep 2 [RNA-Seq]

description: RNA-seq of joints of aged mice injected with lentivirus expressing CLOCK.


title: 201194000041_R04C01

type: genomic

city: Heidelberg

first: Pascal

middle: David

last: Johann

address: Im Neuenheimer Feld 580

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized according to Illumina's standard protocol

scan_protocol: Arrays were imaged using BeadArray reader

data_processing: R library minfi

source_name: Tumor resection

label_protocol: Standard Illumina protocol

extract_protocol: DNA isolation using Dneasy blood and tissue isolation kit (Qiagen)

value: leukemia

tag: patient id

value: 6 years


title: U87-NC_T1-1, biological rep1

description: Gene expression data from U87-NC cells


title: U87-PCGF1-shRNA_T0-2, biological rep2

description: Gene expression data from U87-PCGF1-shRNA cells

value: PCGF1 knockdown


title: U87-PCGF1-shRNA_T0-3, biological rep3


title: 101231000061_R02C01

value: histiocytic sarcoma

value: female

value: 11 years


title: U87-PCGF1-shRNA_T0-1, biological rep1


title: joints of aged mice injected with lentivirus expressing CLOCK  rep 1 [RNA-Seq]


title: P2_AC_2: patient_2_acute_rep 2

value: male

value: peripheral blood leukocytes


title: 201194000001_R02C01


title: transfection_BJAB_3_unstim

source_name: Human Burkitt lymphoma B cell line.

tag: stim condition

value: BJAB

value: transfection


title: 101231000061_R03C01


title: P3_AC_1: patient_3_acute_rep 1


title: Time 0_Control_Rep 2

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 0, Rep 2

value: Blood-stage Nf54 attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit

value: Time 0


title: transfection_BJAB_2_unstim

tag: cell line


title: CD8CART-ND2-Day6-28YMFMz

first: Aviv

last: Madar

address: 250 Massachusetts Ave

institute: Novartis Institutes for Biomedical Research

description: Genetically modified to express chimeric antigen receptors

data_processing:
Starting with raw data. Filtering step: We define "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads. They need to be removed before downstream analysis to decrease data noise. Filtering steps are as follows:  1) Remove reads with adaptors;  2) Remove reads in which unknown bases are more than 10%;  3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).
After filtering, the remaining reads are called "clean reads" and stored as FASTQ format
Reads Mapping: We used Bowtie2 to map clean reads to reference gene. Bowtie2 parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
FPKM were calculated using RSEM
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Tab Separated Values containing genes FPKM values

molecule: polyA RNA

source_name: CD8+ T cells

growth_protocol: Blood samples were obtained from the Human Immunology Core of the University of Pennsylvania. Peripheral blood CD4+ and CD8+ T cells from two different normal donors were negatively isolated using RosetteSep Kits (Stem cell Technologies). Cells were cultured in RPMI 1640 media supplemented with 10% FCS, 100-U/ml penicillin, 100 g/ml streptomycin sulfate, 10 mM HEPES in a 37°C and 5% CO2 incubator.  For stimulation, CD4+ and CD8+ T cells were cultured with activating beads coated with antibodies to CD3 and CD28 at a 1:3 cell to bead ratio. Approximately 24 h after activation, T cells were transduced with lentiviral vectors at an MOI of 5. Lentiviral vectors encoded CAR constructs targeting mesothelin with the SS1 scFv and costimulated by CD28, ICOS and CD28-YMFM (a CD28 mutant with a substitution of an asparagine to phenylalanine in the YMNM motif). For CD8+ T cells, human IL-2 (Chiron) was added every other day to a final concentration of 50 IU/ml. Cells were counted and fed every 2 days and once T cells appeared to rest down, as determined by both decreased growth kinetics and cell size, they were cryopreserved.

extract_protocol:
Frozen CD8+ T cells in RLT buffer were sent to BGI Genomics for RNA extraction, library preparation and sequencing.
1) There are two methods to treat total RNA. Oligo (dT) magnetic beads are used to select mRNA with polyA tail,  or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6) Perform sequencing on prepared library.

treatment_protocol: We used two donors: ND1 and ND2. T cells were collected 6 days after T cell activation. And three groups: CD28z, ICOSz and CD28YMFN-z. CAR-T cell activation: For each donor, CD4+ and CD8+ T cells were mixed at 1:1 ratio. T cells were activated with magnetic beads coated with recombinant mesothelin-Fc at a 1:3 cell:bead ratio. CD8+ T cells were isolated 6 days following activation by negative selection using microbeads. 1x10^6 CD8+ T cells were pelleted, resuspended in RLT buffer and frozen.

tag: group

value: Activated T cells through cognate antigen


title: Time 48_Control_Rep 1

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 48, Rep 1

value: Time 48

tag: treatment

value: Control

value: Rep 1


title: 201194000041_R05C01

value: 10 years


title: P1_REC_2: patient_1_recovery_rep 2

value: after recovery


title: CD8CART-ND2-Day6-28z


title: P1_REC_1: patient_1_recovery_rep 1


title: 201194000001_R03C01


title: transfection_BJAB_3_stim

value: 2.5ug/ml anti-IgM + 2.0 ug/ml anti-CD40 2 hours

tag: vector delivery


title: CD8CART-ND2-Day6-ICOSz


title: Time 32_Control_Rep 1

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 32, Rep 1

tag: time

value: Time 32


title: Time 24_Control_Rep 1

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 24, Rep 1

value: Time 24


title: Time 40_Control_Rep 1

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 40, Rep 1

value: Time 40


title: P1_REC_3: patient_1_recovery_rep 3

source_name: peripheral blood leukocytes

value: female


title: CD8CART-ND1-Day6-ICOSz

value: ICOSz


title: transfection_BJAB_2_stim


title: Time 16_Control_Rep 1

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 16, Rep 1

value: Time 16


title: transfection_BJAB_1_unstim

value: BJAB


title: transfection_BJAB_1_stim

value: transfection


title: CD8CART-ND1-Day6-28z


title: CD8CART-ND1-Day6-28YMFMz


title: P1_AC_3: patient_1_acute_rep 3

value: acute EBV infection

value: peripheral blood leukocytes


title: P1_AC_2: patient_1_acute_rep 2


title: P1_AC_1: patient_1_acute_rep 1


title: Time 08_Control_Rep 1

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 08, Rep 1

value: Blood-stage Nf54 attB P. falciparum parasites cultured in human erythrocytes at 2% hematocrit

value: Time 08


title: Time 0_Control_Rep 1

description: Gene Expression Data

source_name: Nf54 attB parasites,Time 0, Rep 1

value: Time 0

value: Control


title: Rep5_ec_Reb1-BamHI_INO80_20

status: Public on Feb 10 2020

city: Göttingen

first: Elisa

last: Oberbeckmann

address: Justus-von-Liebig Weg 11

department: Molecular Biology

institute: University Medical Center Göttingen

description:
in vitro
plasmid DNA

data_processing:
fastq files were aligned to the SacCer3 (R64), EF2 or E. coli strain B (REL606) genomes using Bowtie (Lengmead et al. 2009). Multiple matches were omited.
BAM files were imported into R Studio (RStudio Team, 2015) using GenomicAlignments (Lawrence et al. 2013). Then, reads were shifted by 73 bp to cover the nucleosome dyad and extended to 50 bp. Genome coverage was caluculated.
Coverage files were either aligned to in vivo +1 nucleosome positions, Reb1 SLIM-ChIP hits (Gutin et al. 2019) or Reb1 PWM hits (Badis et al. 2008), or BamHI cut sites. Signal was normalized per gene in a 2000 bp window around the alignment point.
Genome_build: SacCer3, EF2, Ecoli strain B - REL606
Supplementary_files_format_and_content: bw (big wig) files were generated from genome coverage files using rtracklayer (Lawrence et al. 2009).

organism: Escherichia coli

source_name: in vitro reconstituted chromatin

growth_protocol: Salt Gradient Dialysis: For low, medium and high assembly degrees, 10 µg of plasmid library DNA (pGP546, S. pombe or E. coli) was mixed with ~2, 4 or 8 µg of Drosophila embryo histones, respectively, in 100 µl assembly buffer (10 mM Tris-HCl, pH 7.6, 2 M NaCl, 1 mM EDTA, 0.05% IGEPAL CA630, 0.2 µg BSA). Samples were transferred to Slide-A-lyzer mini dialysis devices, which were placed in a 3 L beaker containing 300 ml of high salt buffer (10 mM Tris-HCl pH 7.6, 2 M NaCl, 1 mM EDTA, 0.05% IGEPAL CA630, 14.3 mM β-mercaptoethanol), and dialyzed against a total of 3 L low salt buffer (10 mM Tris-HCl pH 7.6, 50 mM NaCl, 1 mM EDTA, 0.05% IGEPAL CA630, 1.4 mM β-mercaptoethanol) added continuously via a peristaltic pump over a time course of 16 h under stirring conditions. β-mercaptoethanol was added freshly to all buffers. After complete transfer of low salt buffer, samples were additionally dialyzed against 1 L low salt buffer for 1 h at room temperature. DNA concentration of the SGD chromatin preparations was estimated with a DS-11+ spektrophotometer (Denovix) and if necessary stored at 4 °C for several weeks. To estimate the extend of the assembly degree, an aliquot of the sample was subjected to MNase digestion (as described below) for MNase-ladder read out.

extract_protocol:
Remodeling was started by adding 10 µl SGD chromatin and terminated by adding 0.8 U apyrase followed by incubation at 30 °C for 30 minutes.
For library preparation, approximately 10 - 50 ng of mononucleosomal DNA was incubated with 1.25 U Taq polymerase (NEB), 3.75 U T4 DNA polymerase (NEB) and 12.5 U T4-PNK (NEB) in 1x ligation buffer (B0202S, NEB) for 15 minutes at 12 °C, 15 minutes at 37 °C and 20 minutes at 72 °C. To ligate NEBNext Adaptors (0.75 µM final concentration, from NEBNext Multiplex Oligos Kit) to the DNA, samples were incubated with T4 DNA ligase (NEB) at 25 °C  for 15 minutes, followed by incubation with 2 U USER enzyme (NEB) for 10 minutes at 37°C. Fragments were purified using 2 volumes AMPure XP beads (Beckman Coulter) and amplified for 8-10 cycles using NEBNext Multiplex Oligos, Phusion High-Fidelity DNA Polymerase (1 U, NEB), deoxynucleotide solution mix (dNTP, 2.5 mM, NEB) and Phusion HF Buffer (1x, NEB). The following protocol was applied for amplification: 98 °C for 30 s, 98°C for 10s, 65 °C for 30s, 72 °C for 30s with a final amplification step at 72 °C for 5 minutes. The Qubit dsDNA HS Assay Kit (Invitrogen) was used to assess the DNA content of 1 µL PCR reaction. DNA was purified from agarose gels via PureLink Quick Gel Extraction Kit, measured again with Qubit dsDNA HS Assay Kit and diluted to final concentration of 10 nM (calculation based on the assumption that the DNA fragment length is 272 bp, i. e., 147 bp nucleosomal DNA and 122 bp sequencing adaptor). Diluted samples were pooled according to sequencing reads (~6 Mio reads/ sample). The final pool was quantified by BioAnalyzer (Agilent) and analyzed on an Illumina HiSeq 1500 in the 50 bp single-end mode (Laboratory for Functional Genome Analysis, LAFUGA, LMU Munich).

treatment_protocol: Genome-wide remodeling reaction: All remodeling reactions, except Chd1-containing reactions, were performed at 30 °C in 100 µL with final buffer conditions of 26.6 mM HEPES-NaOH pH 7.5, 1 mM Tris-HCl pH 7.6, 85.5 mM NaCl, 8 mM KCl, 10 mM ammonium sulfate, 10 mM creatine phosphate (Sigma), 3mM MgCl2, 2.5 mM ATP, 0.1 mM EDTA, 0.6 mM EGTA, 1 mM DTT, 14% glycerol, 20 ng/µL creatine kinase (Roche Applied Science). Chd1-containing reactions were performed in 26.6 mM HEPES-NaOH pH 7.5, 1 mM Tris-HCl pH 7.6, 50 mM NaCl, 10 mM creatine phosphate (Sigma), 3 mM MgCl2, 2.5 mM ATP, 0.1 mM EDTA, 0.6 mM EGTA, 1 mM DTT, 14% glycerol, 20 ng/µL creatine kinase. Usually, 10 nM of remodeling enzyme (50 nM Chd1/FACT), 40 nM Reb1 and 20 U of BamHI was added. Before full-length Chd1 (in high-salt buffer) was added to the reaction, it was diluted together with FACT to low salt buffer. For that, full-length Chd1 and purified FACT was mixed in a 1.2:1 ratio in high salt buffer (300 mM NaCl, 20 mM Na·HEPES pH 7.4, 10% (v/v) glycerol, 1 mM DTT), incubated for 5 minutes on ice and then diluted to 30 mM NaCl final concentration.

tag: remodeler

tag: barrier

tag: histone-dna ratio


title: Rep5_ec_Reb1-BamHI_Chd1_80

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_Chd1_40

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_none_40

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_INO80_80

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_ISW1a_40

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_ISW2_80_refill

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_none_80

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_Chd1_80_refill

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_ISW2_40

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_ISW2_20

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_ISW1a_20

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_INO80_40

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_INO80_80_refill

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_ISW1a_80_refill

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_none_20

description:
in vitro
plasmid DNA


title: Rep5_ec_none_none_80

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_Chd1_20

description:
in vitro
plasmid DNA


title: Rep5_ec_none_none_40

description:
in vitro
plasmid DNA


title: Rep5_ec_none_none_20

description:
in vitro
plasmid DNA


title: Rep5_ec_Reb1-BamHI_ISW1a_80

description:
in vitro
plasmid DNA


title: Rep5_ec_none_ISW1a_80

description:
in vitro
plasmid DNA


title: Rep5_ec_none_ISW2_80

description:
in vitro
plasmid DNA


title: Rep5_ec_none_ISW2_40

description:
in vitro
plasmid DNA


title: Rep5_ec_none_ISW1a_20

description:
in vitro
plasmid DNA


title: Rep5_ec_none_INO80_80

description:
in vitro
plasmid DNA


title: P2_AC_1: patient_2_acute_rep 1

value: male


title: Rep5_ec_none_ISW2_20

description:
in vitro
plasmid DNA


title: Rep5_ec_none_ISW1a_40

description:
in vitro
plasmid DNA


title: Rep5_ec_none_Chd1_80_refill

description:
in vitro
plasmid DNA


title: Rep5_ec_none_INO80_20

description:
in vitro
plasmid DNA


title: Rep4_ec_none_none_40

description:
in vitro
plasmid DNA


title: Rep4_ec_none_none_20

description:
in vitro
plasmid DNA


title: Rep4_ec_none_INO80_20

description:
in vitro
plasmid DNA


title: Rep4_ec_none_none_80

description:
in vitro
plasmid DNA


title: Rep4_ec_Reb1_ISW1a_80

description:
in vitro
plasmid DNA


title: Rep4_ec_none_INO80_80

description:
in vitro
plasmid DNA


title: Rep4_ec_Reb1_ISW1a_40

description:
in vitro
plasmid DNA


title: Rep4_ec_Reb1_ISW2_20

description:
in vitro
plasmid DNA


title: Rep4_ec_BamHI_INO80_20

description:
in vitro
plasmid DNA

value: BamHI


title: Rep5_ec_none_INO80_40

description:
in vitro
plasmid DNA


title: Rep3_ec_Reb1_ISW2_80

description:
in vitro
plasmid DNA


title: Rep4_ec_Reb1_INO80_20

description:
in vitro
plasmid DNA


title: Rep3_ec_Reb1_ISW1a_20

description:
in vitro
plasmid DNA


title: Rep4_ec_BamHI_ISW1a_80

description:
in vitro
plasmid DNA


title: Rep4_ec_Reb1_ISW2_80

description:
in vitro
plasmid DNA


title: Rep4_ec_Reb1_INO80_80

description:
in vitro
plasmid DNA


title: Rep5_ec_none_Chd1_80

description:
in vitro
plasmid DNA


title: Rep3_ec_Reb1_INO80_80

description:
in vitro
plasmid DNA


title: Rep3_ec_Reb1_ISW1a_80

description:
in vitro
plasmid DNA


title: Rep5_ec_none_Chd1_20

description:
in vitro
plasmid DNA


title: Rep4_ec_none_ISW1a_40

description:
in vitro
plasmid DNA


title: Rep4_ec_BamHI_INO80_80

description:
in vitro
plasmid DNA


title: Rep3_ec_Reb1_INO80_40

description:
in vitro
plasmid DNA


title: Rep5_ec_none_Chd1_40

description:
in vitro
plasmid DNA


title: Rep3_ec_Reb1_INO80_20

description:
in vitro
plasmid DNA


title: Rep3_ec_Reb1_Chd1_80

description:
in vitro
plasmid DNA


title: Rep3_ec_Reb1_ISW2_20

description:
in vitro
plasmid DNA


title: Rep3_ec_Reb1_Chd1_40

description:
in vitro
plasmid DNA


title: Rep3_ec_none_none_80

description:
in vitro
plasmid DNA


title: Rep3_ec_BamHI_none_40

description:
in vitro
plasmid DNA


title: Rep3_ec_none_INO80_40

description:
in vitro
plasmid DNA


title: Rep3_ec_none_Chd1_80

description:
in vitro
plasmid DNA


title: Rep3_ec_BamHI_ISW1a_20

description:
in vitro
plasmid DNA


title: Rep3_ec_BamHI_Chd1_80

description:
in vitro
plasmid DNA


title: Rep3_ec_none_INO80_80

description:
in vitro
plasmid DNA


title: Rep3_ec_BamHI_INO80_20

description:
in vitro
plasmid DNA


title: Rep3_ec_BamHI_ISW1a_80

description:
in vitro
plasmid DNA


title: Rep3_ec_none_none_20

description:
in vitro
plasmid DNA


title: Rep3_ec_BamHI_INO80_80

description:
in vitro
plasmid DNA


title: Rep3_ec_none_none_40

description:
in vitro
plasmid DNA


title: Rep3_ec_BamHI_ISW2_20

description:
in vitro
plasmid DNA


title: Rep3_ec_BamHI_ISW2_80

description:
in vitro
plasmid DNA


title: isolated_axon

city: Irapuato

first: Cei

last: Abreu-Goodger

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: Langebio - Cinvestav

data_processing:
Bases were called with bcl2fastq ( v2.20.0.422)
Reads were trimmed using Trimmomatic (v.0.36) according to the Ovation SoLo RNA-Seq System instructions. Additionally, we removed adapter sequences and reads shorter than 40 bp.
Trimmed reads were mapped with HISAT2 (v.2.1.0), using default settings apart from --rna-strandness FR, to the Xenopus laevis genome (version 9.1) with an added rRNA contig and subsequently sorted using samtools (v1.6).
Reads mapping to genes were quantified with FeatureCounts (v.1.5.2) using the following parameters: -p -t exon -g gene_id -s 1. Gene models: v1.8.3.2 (Xenbase.org)
The expression levels for each gene were calculated using the rpkm() function from the edgeR package (v.3.20.6).
Genome_build: Xenopus laevis v.9.1
Supplementary_files_format_and_content: tab-delimited text file with FPKM values

organism: Xenopus laevis

source_name: Retinal ganglion cell axon

growth_protocol: Glass-bottom dishes (MatTek) were subsequently coated with poly-L-lysine (Sigma, 10 μg/ml diluted in water) and laminin (Sigma, 10μg/ml diluted in L-15 medium (Gibco). Eyes were dissected from anesthetized embryos, and cultured at 20°C for 20-24 hours in 60% L-15 and 1% Antibiotic-Antimycotic (ThermoFisher).

extract_protocol:
Single Cell RNA Purification Kit (Norgen) was used to extract total RNA from axonal samples following the manufacturer’s instruction. In the lysis step, 200µL of the lysis buffer (Buffer RL, Norgen) were mixed with β-mercaptoethanol (Sigma, 1:100), added to the axonal culture and incubated for 5 minutes. RNA was eluted by applying 9µL Elution Solution twice to the column.
10 ng of axonal RNA collected from isolated axons and SPRI beads (Beckman Coulter) purified were used as input for the Ovation SoLo RNA-Seq System, Custom AnyDeplete (NuGEN) . Using the AnyDeplete system Xenopus laevis rRNA sequences identified through the ncbi nucleotide and the SILVA databases were removed.

treatment_protocol: Axons were severed from the explants at the stereomicroscope by manually cut them with 0.20mm pins and gently removing the dislodged entire eye explant from the plate with a p10 pipette. The complete experimental procedure was concluded within 1.5 hours after the first cut.

value: Retinal ganglion cell axon

tag: strain

value: J-strain

tag: genotype

value: wildtype


title: Rep3_ec_BamHI_INO80_40

description:
in vitro
plasmid DNA


title: Rep3_ec_BamHI_Chd1_40

description:
in vitro
plasmid DNA


title: Rep2_ec_none_INO80_40

description:
in vitro
plasmid DNA


title: CFPAC-1-GR3

city: Hangzhou

first: Jiarong

state: Zhejiang

address: No. 88 Jiefang Road

department: Department of Hepatobiliary and Pancreatic Surgery

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Illumina NovaSeq 6000 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Read quality was checked for each sample using FastQC v0.10.1.
Filter the original fastq file using Seqtk software to get clean reads for data analysis.
High-quality reads were then imported into TopHat v2.0.8 for alignment into BAM files.
Fragments PerKilobase Million (FPKM) values were calculated using a protocol from Robinson et al., Genome Biol, 2010.
Genome_build: hg19, GRCh38
Supplementary_files_format_and_content: Processed gene_expression.txt: Tab-delimited text file includes FPKMs

growth_protocol: All cell lines were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum, 100 µg/mL streptomycin, and 100 IU/mL penicillin and grown in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from gemcitabine-resistant and parental cells. Briefly, cells at 80% of confluence were lysed using TRIzol reagent (Invitrogen) and scraped on ice. The miRNeasy Mini Kit (50) (cat. no. 217004; Qiagen) was used to extract and purify cellular RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two stable gemcitabine-resistant cell lines were established from their corresponding parental cell lines that are relatively sensitive to gemcitabine by continuous exposure to increasing gemcitabine concentrations.

tag: cell type

value: Panceratic cancer cell line

tag: morphology

value: Epithelial

tag: drug sensitivity

value: Resistant


title: Rep2_ec_Reb1_Chd1_40

description:
in vitro
plasmid DNA


title: Rep1_ec_none_none_40

description:
in vitro
plasmid DNA


title: Rep1_ec_none_INO80_40

description:
in vitro
plasmid DNA


title: Rep3_ec_none_Chd1_40

description:
in vitro
plasmid DNA


title: CFPAC-1-GR2


title: CFPAC-1-GR1


title: CFPAC-13

value: Sensitive


title: Rep3_ec_none_INO80_20

description:
in vitro
plasmid DNA


title: Rep2_ec_Reb1_ISW2_40

description:
in vitro
plasmid DNA


title: CFPAC-12


title: Rep2_ec_Reb1_INO80_40

description:
in vitro
plasmid DNA


title: CFPAC-11


title: Rep1_ec_Reb1_INO80_40

description:
in vitro
plasmid DNA


title: BxPC-33


title: BxPC-31


title: BxPC-3-GR2

value: Mesenchymal


title: BxPC-32


title: BxPC-3-GR1


title: 18_S2_WT

first: Gregory

middle: K

last: Tharp

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Ensebl mouse (GRCm38.p3) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: striatum

growth_protocol: All mice were maintained on a 12:12 h light/dark cycle (lights off at 7 p.m.). The temperature was maintained at 22°C plus or minus 1°C with relative humidity (30-70%). All animal procedures were performed in accordance with the NIH and U.S. Public Health Service’s Guide for the care and Use of Laboratory Animals, and were approved by the Institutional Animal Care and Use Committee at Emory University

extract_protocol:
Total RNA was extracted from the cerebellum, prefrontal cortex and striatum of 3-month-old germline SCA17 knock-in mice and age matched wild-type mice (three to four mice per genotype) using Trizol reagent following the manufacturers’ instructions. 1 ug of total RNA for the construction of sequencing libraries.
RNAseq libraries were prepared from 10ng of RNA using the TakaraBio Clontech SMART-Seq v4 kit and Illumina Nextera XT kit.

value: wild type

tag: tissue

value: striatum

tag: age

value: 3 month


title: 19_S3_WT


title: 13_P3_WT

source_name: prefrontal cortex

value: prefrontal cortex


title: 16_S3_KI

value: SCA17 knock-in


title: 11_P1_WT


title: 17_S1_WT


title: 15_S2_KI


title: 9_P2_KI


title: 7_C3_WT

source_name: cerebellum

value: cerebellum


title: 8_P1_KI


title: 10_P3_KI


title: 5_C1_WT


title: 4_C4_KI


title: 3_C3_KI


title: 2_C2_KI


title: BxPC-3-GR3


title: 1_C1_KI


title: Rep9_sc_Reb1-BamHI_wt_80

description:
in vitro
plasmid DNA

organism: Saccharomyces cerevisiae

value: wt


title: 12_P2_WT


title: 14_S1_KI


title: Rep9_sc_Reb1-BamHI_wt_40

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_HQ2_80

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_wt_20

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_HQ2_40_refill

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_HQ2_20

description:
in vitro
plasmid DNA


title: 6_C2_WT


title: Rep9_sc_Reb1-BamHI_HQ1_80

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_HQ2_40

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_HQ1_40_refill

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_HQ1_40

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_HQ1_20

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_wt_40_refill

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_HMGII-HQ2_80

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_HMGII-HQ2_40_refill

description:
in vitro
plasmid DNA


title: GK-S4

first: Meiyi

last: Li

address: No.320 Yueyang Road

institute: Institute of Biochemistry and Cell Biology

description: Whole-genome expression

hyb_protocol: Array hybridization and washing were performed with constant rotation on the whole rat genome gene expression slide (Agilent).

scan_protocol: Slides were scanned by a microarray scanner (Agilent) with default settings.

data_processing:
Data were extracted using the Feature Extraction software program 10.7 (Agilent), and raw data were normalized using the Quantile algorithm, Gene Spring software program 11.0 (Agilent).
Gene Spring software program 11.0 (Agilent).

organism: Rattus norvegicus

source_name: GK rat with RYGB, Intestinal segment, replicate 4

label_protocol: Total RNAs were amplified and labeled with a One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer’s instructions.

growth_protocol: All rats were maintained under constant ambient temperature and humidity with a 12 h light/dark cycle and with free ad lib assess to water and standard laboratory chow unless otherwise specified

extract_protocol: Total RNAs from RL samples were extracted using TRIZOL Reagent (Life Technologies) and checked for a RIN number to inspect the RNA integrity by an Agilent Bioanalyzer 2100 (Agilent Technologies). The qualified total RNAs were further purified using an RNeasy Mini Kit (QIAGEN) and RNase-Free DNase Set (QIAGEN).

treatment_protocol: The RYGB procedures were 30 cm RL in length for the GK_S group. For sham-operated animals (GK-PF), following laparotomy, an incision was made at a site 16 cm distant from the ligament of Treitz and then reconnected by side-to-side anastomosis without intestinal rearrangement. The intestine was gently handled for another 30 min before closure of the incision.

tag: gender

value: male


title: GK-Sham-PF4

description: Whole-genome expression

source_name: GK rat with sham-operation, Intestinal segment, replicate 4


title: GK-Sham-PF5

description: Whole-genome expression

source_name: GK rat with sham-operation, Intestinal segment, replicate 5


title: Rep9_sc_Reb1-BamHI_HMGII-HQ2_20

description:
in vitro
plasmid DNA


title: GK-S2

description: Whole-genome expression

source_name: GK rat with RYGB, Intestinal segment, replicate 2


title: GK-S5

description: Whole-genome expression

source_name: GK rat with RYGB, Intestinal segment, replicate 5


title: GK-S3

description: Whole-genome expression

source_name: GK rat with RYGB, Intestinal segment, replicate 3


title: GK-Sham-PF2

description: Whole-genome expression

source_name: GK rat with sham-operation, Intestinal segment, replicate 2


title: GK-Sham-PF1

description: Whole-genome expression

source_name: GK rat with sham-operation, Intestinal segment, replicate 1


title: SCD mouse lung 2

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

description: Gene expression data from adult aged-matched mice

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)

data_processing: Expression console, Partek Genome Suite 6.6; RMA normalization. significance cut off score was set to <0.05

label: Biotin

source_name: whole lung

label_protocol: 3'IVT gexpress kit (affymetrix)

growth_protocol: adult aged-matched mice were cervically euthanized to obtain whole lung tissue for RNA extraction

extract_protocol: Total RNA was extracted from whole lung isolated from sickle cell and control mice using TRIzol reagent (ThermoFisher Scientific).

value: whole lung

value: SCD Tg


title: Wistar4

description: Whole-genome expression

source_name: Wistar, Intestinal segment, replicate 4


title: Rep9_sc_Reb1-BamHI_HMGII-HQ1_80

description:
in vitro
plasmid DNA


title: Wistar5

description: Whole-genome expression

source_name: Wistar, Intestinal segment, replicate 5


title: Rep9_sc_Reb1-BamHI_HMGII-HQ1_40_refill

description:
in vitro
plasmid DNA


title: WT mouse lung 1

scan_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)


title: GK-S1

description: Whole-genome expression

source_name: GK rat with RYGB, Intestinal segment, replicate 1


title: SCD mouse lung 1


title: GK-Sham-PF3

description: Whole-genome expression

source_name: GK rat with sham-operation, Intestinal segment, replicate 3


title: Rep9_sc_Reb1-BamHI_HMGII-HQ2_40

description:
in vitro
plasmid DNA

source_name: in vitro reconstituted chromatin


title: mES H3K27me3 ChIP-seq

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
All analysis was done using NGseqBasic pipeline, using default parameters   ( http://userweb.molbiol.ox.ac.uk/public/telenius/NGseqBasicManual/external/ )  Including the following steps :
mapping : bowtie -m 2 --maxIns 350
for un-mapping reads : trim_galore -- length 10, flash -m 9 -x 0.125
combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
removing read pairs overlapping Duke Blacklisted regions
removing duplicates : samtools rmdup
reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
pileup of fragments (bedtools genomecov -counts)
generating bigwig tracks (ucsctools bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig of Reconstructed sequenced fragments

source_name: Embryonic stem cells

growth_protocol: Embryonic stem cells were grown in GMEM media containing FCS, Glutamine/Pen-Strep , Sodium pyruvate, non-essential amino acids and LIF.

extract_protocol:
Cultured cells were harvested and formaldehyde fixed (1%) and processed for ChIP experiments.
ChIPs were performed according to the Millipore ChIP protocol, as described previously (De Gobbi et al., 2007). For ChIP-Seq experiments, Embryonic Stem cells were fixed with 1% formaldehyde for 10 minutes at RT and chromatin was sonicated to a size <500 bp. Immunoprecipitations were performed, after an overnight incubation with the appropriate antibody, followed by protein A agarose bead incubation (Millipore). Agarose beads are then washed and eluted and immunoprecipitated DNA  purified by phenol and chloroform extraction followed by ethanol precipitation.
The library was constructed using Illumina protocol. The library was amplified prior to size selection (150-200bp).  Model- GAIIx Chemistry-SBS v4 cBot single generation kit with v4 flow cell SCS 2.8 RTA 1.8 Recipe v7.4

treatment_protocol: No treatment

value: Embryonic stem cells

tag: chip antibody

value: antiH3K27me3 Millipore (used to be Upstate) catalog number 07-449 lot DAM1641103


title: WT mouse lung 2


title: Wistar3

description: Whole-genome expression

source_name: Wistar, Intestinal segment, replicate 3


title: Rep9_sc_Reb1-BamHI_HMGII-HQ1_40

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_HMGII_80

description:
in vitro
plasmid DNA

value: HMGII


title: Wistar2

description: Whole-genome expression

source_name: Wistar, Intestinal segment, replicate 2


title: APL_GFP-_S44

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

institute: Heidelberg University

description: nuclear RNA

data_processing:
Araport11 gene annotation file was taken (Araport11_GFF3_genes_transposons.201606.gtf).
FASTQ files were trimmed by Cutadapt (v2.3) using following options -g AAGCAGTGGTATCAACGCAGAGTACGGG -a CCCGTACTCTGCGTTGATACCACTGCTT -g AAGCAGTGGTATCAACGCAGAGTAC  -a GTACTCTGCGTTGATACCACTGCTT -b "A 30" -b "T 30 " -n 2 -g AGATCGGAAGAGC -l 50 -m 23 --overlap 5. By these options, oligo sequence used in Smart-seq2 amplification, poly A or T sequence, Illumina adaptor sequence were removed from the reads.
Trimmed files were then mapped to the genome by STAR (v2.5.0a) using --outFilterMultimapNmax 1 --alignIntronMax 10000 --alignMatesGapMax 10000 --outFilterScoreMinOverLread 0.9 options.
For GFP reads, GFP sequence was indexed by STAR using –genomeSAindexNbases 4 option, and then reads were mapped using STAR with --alignIntronMax 1 --alignMatesGapMax 1 --outFilterScoreMinOverLread 0.90 options.
Further analysis was carried out in R (v3.5.0). GTF file was imported using makeTxDbFromGRanges in GenomicFeatures library (v1.32.3) with drop.stop.codons option. Position of each gene was extracted by genes function, which also includes the intron region. Reads counts per gene were obtained using summarizeOverlaps in GenomicAlignments library (v1.16.0) with mode = "Union", ignore.strand = TRUE options. Only genes of Arabidopsis was kept, and GFP reads were added in the last line in rawCounts table for selected samples. bigWig files were generated by bamCoverage in deepTools from bam files.
Genome_build: Arabidopsis Tair 10
Supplementary_files_format_and_content: Csv files include raw counts values for each Sample. bigWig files are generated from bam files for coverage tracks.

organism: Arabidopsis thaliana

source_name: Inflorescence stem nuclei

growth_protocol: Arabidopsis were grown on soil for three weeks in short days (8h light 16h dark, constant 21°C) and then transfered to long days (16h light 8h dark) to stimulate flowering.

extract_protocol:
2nd internode of Arabidopsis inflorescence stem were collected in a petri dish on ice. 2ml cold isolation buffer (20mM Tris (pH=7.5), 40mM NaCl, 90mM KCl, 2mM EDTA (pH=8.0), 0.5mM EGTA, 0.05% Triton X-100, 0.5mM Spermidine, 0.2mM Spermine, 15mM 2-Mercaptoethanol, 0.5mM PMSF, cOmplete Protease Inhibitor Cocktail (Roche, #11697498001)) supplemented with 10µl RiboLock RNase inhibitor (40U/µL) (ThermoFisher, #EO0381) was added to 2g of stem. Samples were chopped manually on ice for 10 min. Nuclei were collected by centrifuge (1000g, 10min, 4°C) and gently washed by cold resuspension buffer (same formula as isolation buffer but without Triton X-100) for two times. 300µl of resuspension buffer supplemented with 10µg/ml Hoechst 33342 at final concentration and 5µl RiboLock RNase inhibitor were added to the centrifuged nuclei. 15,000 nuclei were sorted into TRIzol solution as a replicate sample by BD FACSAriaTM IIIu cell sorter using a 70 µm sort nozzle according to GFP signal level, except for LTP1_GFP+_S21 which was 10,800 nuclei. RNA was extracted into 15 µl water according to manufacture's protocol.
1 µl was used for mRNA-seq library construction by Smart-seq2 protocol (Picelli et al., Nature Methods, 2013; Hofmann et al., Plant Reprod., 2019). NEBNext Ultra II gDNA prep kit with the NEBNext Multiplex Oligos for Illumina was used for library preparation

tag: sample type

value: GFP negative


title: APL_GFP-_S43

description: nuclear RNA


title: APL_GFP-_S45

description: nuclear RNA


title: Rep9_sc_Reb1-BamHI_HMGII-HQ1_20

description:
in vitro
plasmid DNA


title: Wistar1

description: Whole-genome expression

source_name: Wistar, Intestinal segment, replicate 1


title: SMXL5_GFP-_S42

description: nuclear RNA


title: SMXL5_GFP-_S41

description: nuclear RNA


title: Rep9_sc_Reb1-BamHI_HMGII_40

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_DN-Ino80_80

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_HMGII_20

description:
in vitro
plasmid DNA


title: SMXL5_GFP-_S40

description: nuclear RNA


title: Rep9_sc_Reb1-BamHI_DN-Ino80_40

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_DN-Ino80_20

description:
in vitro
plasmid DNA


title: NST3_GFP-_S48

description: nuclear RNA


title: NST3_GFP-_S47

description: nuclear RNA


title: Rep9_sc_Reb1-BamHI_DNhp10_80

description:
in vitro
plasmid DNA


title: LTP1_GFP+_S21

description: nuclear RNA

value: GFP positive


title: Rep9_sc_Reb1-BamHI_DNhp10_20

description:
in vitro
plasmid DNA


title: SCR_GFP+_S18

description: nuclear RNA


title: LTP1_GFP+_S19

description: nuclear RNA


title: LTP1_GFP+_S20

description: nuclear RNA


title: Rep9_sc_Reb1-BamHI-BamHI_ct_20

description:
in vitro
plasmid DNA

value: ct


title: Rep9_sc_Reb1-BamHI_DNhp10_40

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_ct_80

description:
in vitro
plasmid DNA


title: SCR_GFP+_S16

description: nuclear RNA


title: PXY_GFP+_S9

description: nuclear RNA


title: SCR_GFP+_S17

description: nuclear RNA


title: Rep9_sc_none_wt_20

description:
in vitro
plasmid DNA


title: Rep9_sc_none_wt_40

description:
in vitro
plasmid DNA


title: Rep9_sc_none_none_80

description:
in vitro
plasmid DNA


title: PXY_GFP+_S8

description: nuclear RNA


title: PXY_GFP+_S7

description: nuclear RNA


title: VND7_GFP+_S6

description: nuclear RNA


title: VND7_GFP+_S5

description: nuclear RNA


title: Rep9_sc_none_none_20

description:
in vitro
plasmid DNA


title: Rep9_sc_none_HQ2_80

description:
in vitro
plasmid DNA


title: NST3_GFP-_S46

description: nuclear RNA


title: VND7_GFP+_S4

description: nuclear RNA


title: Rep9_sc_none_HQ2_20

description:
in vitro
plasmid DNA


title: Rep9_sc_none_HQ2_40

description:
in vitro
plasmid DNA


title: Rep9_sc_Reb1-BamHI_ct_40

description:
in vitro
plasmid DNA


title: Rep9_sc_none_HQ1_80

description:
in vitro
plasmid DNA


title: APL_GFP+_S14

description: nuclear RNA


title: APL_GFP+_S13

description: nuclear RNA


title: SMXL5_GFP+_S12

description: nuclear RNA


title: APL_GFP+_S15

description: nuclear RNA


title: Rep9_sc_none_HQ1_20

description:
in vitro
plasmid DNA


title: Rep9_sc_none_HQ1_40

description:
in vitro
plasmid DNA


title: Rep9_sc_none_wt_80

description:
in vitro
plasmid DNA


title: Rep9_sc_none_HMGII-HQ2_80

description:
in vitro
plasmid DNA


title: SMXL5_GFP+_S10

description: nuclear RNA


title: NST3_GFP+_S2

description: nuclear RNA


title: NST3_GFP+_S1

description: nuclear RNA


title: NST3_GFP+_S3

description: nuclear RNA


title: SMXL5_GFP+_S11

description: nuclear RNA


title: Rep9_sc_none_none_40

description:
in vitro
plasmid DNA


title: Rep9_sc_none_HMGII-HQ2_40

description:
in vitro
plasmid DNA


title: Rep9_sc_none_HMGII-HQ1_80

description:
in vitro
plasmid DNA


title: Rep9_sc_none_HMGII-HQ2_20

description:
in vitro
plasmid DNA


title: Rep9_sc_none_HMGII-HQ1_40

description:
in vitro
plasmid DNA


title: shCtrl-neg-2

city: Boston

first: Jesse

last: Poganik

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital, Harvard Medical School

data_processing:
Reads were trimmed for low quality and adaptor sequences with cutadapt v1.8 [parameters: –m 50 –q 20 –a AGATCGGAAGAGCACACGTCTGAACTCCAGTC –match-read-wildcards (Martin, 2011)].
Trimmed reads were mapped to rRNA sequences with bowtie2 v2.2 to remove them [Parameters: default mapping options,  –al and –un to split matching and non-matching reads (Langmead and Salzberg, 2012)].
Reads were mapped to the reference genome/transcriptome (GRCh37/hg19]) using tophat v2.1 [parameters: –library-type=fr-firststrand –no-novel-juncs –G <ref_genes.gtf> (Kim et al., 2013)].
Cufflinks v2.2 (cuffnorm/cuffdiff) was used to generate FPKM values and statistical analysis of differential gene expression (Trapnell et al., 2013).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix tables of raw counts and FPKMs

growth_protocol: HEK293T (obtained from ATCC) were cultured in MEM (Gibco 51090036) supplemented with 10% v/v fetal bovine serum (Sigma), penicillin/streptomycin (Gibco), sodium pyruvate (Gibco), and non-essential amino acids (Gibco) at 37°C in a humidified atmosphere of 5% CO2.  Media was changed every 2-3 days.

extract_protocol:
Cells were lysed by the addition of Trizol (Invitrogen) and RNA was isolated following the manufacturer’s protocol. The quality of the RNA was assessed by Nanodrop spectrophotometry (A260/A280 ratio ~2) and fragment analysis using a Bioanalyzer (Agilent). RQN for all samples was 10.0.
Library construction and sequencing were performed by the RNA sequencing core (RSC) service at Cornell University. Briefly, ribosomal (r)RNA was subtracted by hybridization from total RNA samples (100 ng total RNA input) using the RiboZero Magnetic Gold H/M/R Kit (Illumina). Following cleanup by precipitation, rRNA-subtracted samples was quantified with a Qubit 2.0 (RNA HS kit; Thermo Fisher). TruSeq-barcoded RNAseq libraries were generated from half of the rRNA-subtracted samples with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). Each library was quantified with a Qubit 2.0 (dsDNA HS kit; Thermo Fisher) and the size distribution was determined with a Fragment Analyzer (Advanced Analytical) prior to pooling.Libraries were sequenced on a NextSeq500 instrument (Illumina). At least 60M single-end 75bp reads were generated per library.

treatment_protocol: Generation of shRNA-based knockdown cell lines: HEK293T packaging cells (5.5 × 105 cells) were seeded in 6-well plates in antibiotic-free media and incubated for 24 h. The cells were transfected with a mixture of 500 ng packaging plasmid (pCMV-R8.74psPAX2), 50 ng of envelope plasmid (pCMV-VSV-G) and 500 ng of pLKO vector containing the hairpin sequence (Sigma; shHuR:  5′–CCGGCCCATCACAGTGAAGTTTGCACTCGAGTGCAAACTTCACTGTGATGGGTTTTT–3′; shControl: 5′– GTCGAGCTGGACGGCGACGTA–3′) using TransIT-LT1 (Mirus Bio) following the manufacturer’s protocol. shControl plasmid was obtained from Prof. Andrew Grimson (Cornell University). 18 h-post transfection, the media was replaced with media containing 20% FBS and incubated for a further 24 h.  Media containing virus particles was harvested, centrifuged (800×g, 10 min), filtered through 0.45 m filter, and used for infection or frozen at –80°C for later use. HEK293T cells (5.5 × 106 cells) in 6-well plates were treated with 1 mL of virus-containing media in a total volume of 6 mL of media containing 8 g/mL polybrene.  After 24 h, media was changed and the cells were incubated for 24 h.  Following this period, media was changed to media containing 2 g/mL puromycin (Santa Cruz). Following selection, cells were assayed by western blotting.  Small molecule treatment: HEK293T shHuR or shControl cells in 6-well plates were treated with HNE(alkyne) (25 μM; Cayman Chemical) or H2O2 (225 μM; Sigma) supplemented in the growth media for 18 h prior to RNA isolation.

tag: cell line

tag: genotype/variation

value: expressing shControl

tag: small-molecule treatment

value: none (untreated control)


title: Rep9_sc_none_HMGII-HQ1_20

description:
in vitro
plasmid DNA


title: Rep9_sc_none_HMGII_40

description:
in vitro
plasmid DNA


title: shCtrl-neg-1


title: Rep9_sc_none_DN-Ino80_80

description:
in vitro
plasmid DNA


title: shCtrl-HNE-2

value: HNE(alkyne) (25 micromolar)


title: shCtrl-H2O2-2

value: H2O2 (225 micromolar)


title: shCtrl-H2O2-1


title: shHuR-neg-1

value: expressing shHuR


title: Rep9_sc_none_DNhp10_80

description:
in vitro
plasmid DNA


title: shHuR-HNE-1


title: shHuR-H2O2-1


title: Rep9_sc_none_DN-Ino80_40

description:
in vitro
plasmid DNA


title: Rep9_sc_none_ct_80

description:
in vitro
plasmid DNA


title: Rep9_sc_none_ct_40

description:
in vitro
plasmid DNA


title: Rep9_sc_none_DNhp10_40

description:
in vitro
plasmid DNA


title: shHuR-neg-2


title: Rep9_sc_none_DNhp10_20

description:
in vitro
plasmid DNA


title: shCtrl-HNE-1


title: Rep8_sc_Reb1-BamHI_HQ2_80

description:
in vitro
plasmid DNA


title: Rep8_sc_Reb1-BamHI_HQ2_40

description:
in vitro
plasmid DNA


title: Rep9_sc_none_ct_20

description:
in vitro
plasmid DNA


title: MuSC.inj.d1.Muscle#3

first: CBDM

last: Lab

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Day 1 post-cardiotoxin injury

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Hindlimb skeletal muscle

extract_protocol:
1,000 cells were double-sorted by Moflo Astrios cell sorter into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X25bp reads.

value: Hindlimb skeletal muscle

value: 8 weeks


title: MuSC.d0.Muscle#3

description: Uninjured


title: MuSC.inj.d1.Muscle#2

description: Day 1 post-cardiotoxin injury


title: Rep9_sc_none_HMGII_80

description:
in vitro
plasmid DNA


title: Rep9_sc_none_HMGII_20

description:
in vitro
plasmid DNA


title: MuSC.inj.d1.Muscle#1

description: Day 1 post-cardiotoxin injury


title: shHuR-H2O2-2


title: Rep8_sc_Reb1-BamHI-BamHI_HQ1_80

description:
in vitro
plasmid DNA


title: MuSC.d0.Muscle#2

description: Uninjured


title: Rep9_sc_none_DN-Ino80_20

description:
in vitro
plasmid DNA


title: Rep8_sc_Reb1-BamHI_HQ1_40

description:
in vitro
plasmid DNA


title: MuSC.d0.Muscle#1

description: Uninjured


title: Rep8_sc_Reb1-BamHI_HQ1_20

description:
in vitro
plasmid DNA


title: shHuR-HNE-2


title: MSC.inj.d1.Muscle#3

description: Day 1 post-cardiotoxin injury


title: Rep8_sc_Reb1-BamHI_HMGII_80

description:
in vitro
plasmid DNA


title: Rep8_sc_Reb1-BamHI_HMGII_40

description:
in vitro
plasmid DNA


title: MSC.d0.Muscle#3

description: Uninjured


title: MSC.inj.d1.Muscle#1

description: Day 1 post-cardiotoxin injury


title: CD45+.inj.d1.Muscle#3

description: Day 1 post-cardiotoxin injury


title: MSC.d0.Muscle#2

description: Uninjured


title: MSC.d0.Muscle#1

description: Uninjured


title: CD45+.inj.d1.Muscle#2

description: Day 1 post-cardiotoxin injury


title: CD45+.d0.Muscle#3

description: Uninjured


title: Rep8_sc_none_HQ1_40

description:
in vitro
plasmid DNA


title: CD45+.inj.d1.Muscle#1

description: Day 1 post-cardiotoxin injury


title: Rep8_sc_Reb1-BamHI_allQ_40

description:
in vitro
plasmid DNA

value: allQ


title: Rep8_sc_none_HQ1_80

description:
in vitro
plasmid DNA


title: Rep8_sc_none_HQ2_80

description:
in vitro
plasmid DNA


title: Rep8_sc_Reb1-BamHI_DNhp10_80

description:
in vitro
plasmid DNA


title: Rep8_sc_none_HQ2_20

description:
in vitro
plasmid DNA


title: CD45+.d0.Muscle#2

description: Uninjured


title: Rep8_sc_none_HQ1_20

description:
in vitro
plasmid DNA


title: Rep8_sc_Reb1-BamHI_DNhp10_40

description:
in vitro
plasmid DNA


title: Rep8_sc_none_HQ2_40

description:
in vitro
plasmid DNA


title: CD45+.d0.Muscle#1

description: Uninjured


title: CD31+.inj.d1.Muscle#3

description: Day 1 post-cardiotoxin injury


title: Rep8_sc_none_DNhp10_80

description:
in vitro
plasmid DNA


title: Rep8_sc_none_HMGII_40

description:
in vitro
plasmid DNA


title: MSC.inj.d1.Muscle#2

description: Day 1 post-cardiotoxin injury


title: CD31+.inj.d1.Muscle#1

description: Day 1 post-cardiotoxin injury


title: Rep8_sc_none_DNhp10_40

description:
in vitro
plasmid DNA


title: Rep8_sc_none_allQ_80

description:
in vitro
plasmid DNA


title: CD31+.d0.Muscle#2

description: Uninjured


title: CD31+.d0.Muscle#3

description: Uninjured


title: Rep8_sc_Reb1-BamHI_allQ_80

description:
in vitro
plasmid DNA