title: sequencing of CGA-1-1 gene in HeLa-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat1

description:
SerCGAsgRNA_d8_CGA-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: RNA_Th2_120h_rep2

status: Public on Dec 22 2020

type: SRA

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

library_source: transcriptomic

data_processing:
ATAC-seq and ChIP-seq read sequences (61 bp) were aligned to the mm9 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (v2.4.2.6) MACS2 and Homer.
RNA-seq read sequences (61 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (v2.4.2.6) and TopHat (version 1.3.2).
Genome_build: ATAC-seq,ChIP-seq; mm9, RNA-seq; mm10
Supplementary_files_format_and_content: ATAC-seq and ChIP-seq bigwig files were generated using deeptools v3.1.
RNA-seq text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Primary splenic CD4 T cells

growth_protocol: Splenic CD44low CD62Lhi CD4+ cells were stimulated under Th2 culture conditions (30 U/ml IL-2 culture sup, 100 U/ml IL-4, and 10 µg/ml anti-IFN-γ Ab)  in vitro.

extract_protocol:
ATAC-seq; Fifty thousand cells were pelleted and washed with 50 μl of 1× PBS, followed by treatment with 50 μl of lysis buffer. The nuclei were re-suspended in 40 μl of TDE buffer with 2 μl of Tn5 transposase (15027865, 15027866; Illumina) to tag and fragmentize the accessible chromatin. The reaction was incubated at 37°C with shaking at 300 rpm for 30 minutes. The fragmentized DNAs were purified using a QIAGEN MinElute kit and amplified with 11 or 12 PCR cycles, based on the amplification curve. ChIP-seq; 1–10×10e6 cells were fixed with 1% paraformaldehyde at 37°C for 10 min. Cells were sedimented, washed, and lysed with SDS lysis buffer (50 mM Tris-HCl, 1% SDS, 10 mM EDTA, 1 mM PMSF, 1 mg/ml aprotinin, and 1 mg/ml leupeptin). The lysates were sonicated to reduce the DNA lengths to between 200 and 1000 bps. The soluble fraction was diluted in ChIP dilution buffer and incubated with Ab conjugated with Dynabeads protein A and G overnight at 4°C. The immune complexes were then captured using a magnet and washed with low-salt, high-salt, LiCl, and Tris–EDTA wash buffer. Enriched chromatin fragments were eluted with elution buffer (0.1 M NaHCO3 containing 1% SDS). The eluted material was incubated at 65°C for 6 h to reverse the formaldehyde cross-links and treated with RNase A (10 mg/ml) and Proteinase K (40 mg/ml). DNA was extracted with a QIAquick PCR purification kit (QIAGEN). RNA-seq; Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
ATAC-seq; The libraries were sequenced for 50 cycles (paired-end reads) on an Illumina HiSeq 1500. ChIP-seq; Ab-specific immunoprecipitates and total input DNA samples were prepared using a SMARTer ThruPLEX DNA-Seq Kit (TaKaRa). RNA-seq; TruSeq Stranded mRNA Library Preparation Kit (Illumina) was used according to the manufacturer's protocol.

tag: strain

tag: cell type

value: Primary splenic CD4 T cells

tag: time

tag: differentiation

tag: genotype

value: WT

tag: stimulation

value: regular

tag: in vitro, in vivo

value: in vitro


title: RNA_Th2_48h_prolong_rep2

value: prolong


title: S18

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava.
Illumina adapter contaminations were removed from reads using Cutadapt.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM.
Genome_build: GRCm38 assembly, Ensembl genebuild 91
Supplementary_files_format_and_content: ALL.GRCm38_91.rsem.genes.results.txt file contains ENSEMBL gene and transcript Ids and RSEM estimated counts for each gene and sample.

molecule: polyA RNA

source_name: Posterior somites region

extract_protocol:
Sample preparation: Embryos were retrieved from the uterus of pregnant females at E9 and the regions analyzed mechanically dissected.
RNA was isolated using RNeasy Micro Kit RNA Isolation Kit (QIAGEN)
RNA-seq libraries were generated using the NEBNext library preparation kit (Illumina).
Libraries were sequenced (single-end mode and length of 61 bp) on the Illumina HiSeq 2500 system.

tag: tissue

value: embryo

tag: region

value: Posterior somites

value: Control

tag: gender

value: Male

tag: embryonic stage

value: 23 somites


title: shRNPDL KD rep1

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using tophat2 --no-discordant --read-edit-dist 4 -N 4 --b2-N 1. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue < =0.01
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

organism: Homo sapiens

source_name: Cervical cancer cell HeLa

growth_protocol: HeLa cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
The HeLa cells were ground into fine powder before RNA extraction. Total RNA was extracted by the hot phenol method. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 10μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.  For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. Illumina HiSeq 4000 was used to collect data from 150-bp pair-end sequencing (ABlife Inc., Wuhan, China).

treatment_protocol: shRNA transfection of HeLa cells was performed using lipofectAMINE 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for q-PCR analysis.

tag: cell line

value: HeLa

tag: genotype/variation

value: shRNPDL knock down


title: sequencing of CGA-4-1 gene in HeLa-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat1

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

country: Israel

institute: Agriculture Research Organization

description:
SerCGAsgRNA_d4_CGA-4-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

library_source: genomic

data_processing:
library strategy: amplicon library
Read were trimmed using cutadapt
NHEJ events were quantified using CRISPResso (Pinello et al., 2016)  in the CRISPR-iCas9 targeted samples. The input for the CRISPResso pipeline included both the amplicon sequences of the unedited (WT) tRNA genes and the sgRNA sequences. The minimum identity score for the alignment was set to 0
Genome_build: hg19
Supplementary_files_format_and_content: Read count of WT reads or reads with NHEJ events. Read count of reads with insertions and deletions for the NHEJ reads was calculated as well.

molecule: genomic DNA

source_name: HeLa iCas9 - SerCGA sgRNA

growth_protocol: HeLa- iCas9 with single sgRNAs  cells (targeteing 4 different human tRNA families) were grown in DMEM + NEAA (Life Technologies; 10938-025) - Dulbecco’s Modified Eagle medium with 4.5mg/ml D-Glucose and Non-Essential amino acids. Supplemented with 10% FBS, 1% penicillin/ streptomycin (P/S), 1% L-Glutamine and 1% Sodium Pyruvate. The medium was supplemented with 200µg/ml Hygromycin (for iCas9 selection, Thermo Fisher; 10687010), 2µg/ml Puromycin (for sgRNA selection, Sigma-Aldrich; 58-58-2) and 1µg/ml Doxycycline (for iCas9 induction, Sigma-Aldrich; 10592-13-9).   WI38 fast iCas9 with single sgRNAs cells (targeteing 2 different human tRNA families) were grown in in MEM-EAGLE + NEAA– Earle’s salts base with Non-Essential amino acids (Biological Industries; 01-025-1A), supplemented with 10% FBS, 1% penicillin/ streptomycin (P/S) and 1% L-Glutamine. The medium was supplemented with 200µg/ml Hygromycin (for iCas9 selection, Thermo Fisher; 10687010), 10 µg/ml Blasticidin (for sgRNA selection, InvivoGen; BLL-38-02A)  and 1µg/ml Doxycycline (for iCas9 induction, Sigma-Aldrich; 10592-13-9).   Upon iCas9 induction, each cell population was samples every 4 days, and fresh medium containing all  antibiotics was replaced every two days for 12 days.

extract_protocol:
PureLink genomic DNA mini kit (Invitrogene; K182000)
genomic DNA was used as template for PCR to amplify specifically the tRNA isodecoder genes of the CRISPR- targeted tRNAs in the population. PCR reaction was conducted using KAPA HiFi HotStart ReadyMixPCR (X2) (kapabiosystems; KK2601), 10µM of each primer and 100ng of genomic DNA in a 60µl total volume reaction, for 25 cycles. Primers and annealing temperatures are listed (Figure2- source data 1). After PCR validation using agarose gel, the PCR product was purified with SPRI-beads using left-side size selection protocol in which the PCR product and beads were mixed at 1:1.5 ratio. Then, each sample was barcoded with a different Illumina barcode while the Forward primer was fixed and the reverse primer included the different barcodes. The barcoding PCR reaction that was conducted using KAPA HiFi HotStart ReadyMixPCR Kit (X2), 10µM of Illumina primers and 0.35-0.7ng of PCR product in a 10µl total volume reaction, for 15 cycles. Additional clean-up step was performed using SPRI beads with left-side size selection protocol in which the PCR product and beads were mixed at 1:1.5 ratio. Samples were pooled in equal amounts and sequenced.

treatment_protocol: Cells were centrifuged for 3 minutes at 2000rpm. The medium was removed and cell pellet was freezed at -80°C until genomic DNA extraction.

tag: crispr construct

value: iCas9 - SerCGA sgRNA

tag: icas9 induction

value: Day 4

tag: the sequenced trna gene

tag: repeat


title: shRNPDL KD rep2


title: sequencing of CGA-3-1 gene in HeLa-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat2

description:
SerCGAsgRNA_d4_CGA-3-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: repeat 2


title: RNA_Th2_120h_rep1

tag: strain


title: S17

source_name: Anterior somites region

value: Anterior somites


title: sequencing of CGA-3-1 gene in HeLa-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat1

description:
SerCGAsgRNA_d4_CGA-3-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: RNA_Th2_120h_prolong_rep1

tag: cell type


title: sequencing of CGA-2-1 gene in HeLa-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat2

description:
SerCGAsgRNA_d4_CGA-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: S16

value: Female

value: 21 somites


title: S15


title: S14

value: DKO


title: sequencing of CGA-1-1 gene in HeLa-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat2

description:
SerCGAsgRNA_d4_CGA-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: sequencing of CGA-4-1 gene in HeLa-iCas9-SerCGA sgRNA cells, before iCas9 induction, repeat2

description:
SerCGAsgRNA_d0_CGA-4-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: Day 0


title: sequencing of CGA-2-1 gene in HeLa-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat1

description:
SerCGAsgRNA_d4_CGA-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: sequencing of CGA-1-1 gene in HeLa-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat1

description:
SerCGAsgRNA_d4_CGA-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: sequencing of CGA-4-1 gene in HeLa-iCas9-SerCGA sgRNA cells, before iCas9 induction, repeat1

description:
SerCGAsgRNA_d0_CGA-4-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: RNA_Th2_0h_rep2

growth_protocol: Splenic CD44low CD62Lhi CD4+ cells were sorted by cell sorter.

value: Primary splenic CD4 T cells

tag: time

value: WT

value: regular

value: in vitro


title: Murine heart tissue from infected mice, uninfected control [S_01]

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

data_processing:
FASTQ files were aligned to Genome data base using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/],and read counts obtained for each gene
Differential Expression was estimated using DESeq2 [https://www.ncbi.nlm.nih.gov/pubmed/25516281] and edgeR [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/]
Genome_build: Mus_musculus.GRCm38.94.gtf
Supplementary_files_format_and_content: A plain text file (*.txt) was generated per sample, consisting in two columns: first column contains gene IDs (ensembl_ID), and second column the number of raw counts obtained by STAR per gene.

source_name: Heart

growth_protocol: Mice were breed and housed at the Animal Facility of CIC bioGUNE under controled conditions according to the animal care international gidelines.

extract_protocol:
RNA was extracted from the 3th top of the heart (base) using the Allprep DNA/RNA/miRNA Universal kit (Qiagen)
Sequencing libraries were prepared following the protocol "TruSeqStrandedmRNASamplePreparationGuide(Part#15031047Rev.E)" with the "TruSeq stranded mRNAseq library preparation kit” (Illumina Inc., Cat.#RS-122-2101orRS-122-2102(SetAorB,respectively))

treatment_protocol: Mice were infected with 100,000 Borrelia burdorferi in the midline of the back. In the groups treated with 3-PO, the mice were injected twice per week during 3 weeks with 50 mg/kg of 3-PO, starting 14 days after infection

tag: time of infection

tag: agent

tag: treatment


title: RNA_Th2_0h_rep1

tag: differentiation

tag: genotype

tag: stimulation

tag: in vitro, in vivo


title: SAMPLE 22_KO-CYP2C70_UDCA Feeding 0.1%

type: RNA

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

description: RMA - PLM (unlogged scale): 22-m23_(MoGene-2_0-st).CEL (KO_UDCA)

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on MoGene-2_0-st Chip. GeneChips were washed and stained in the Affymetrix Fluidics

scan_protocol: Affymetrix GeneChip Scanner 7G and Affymetrix GeneChip Command Console software (AGCC)

data_processing: The data where normalized using RMA (PLM) normalisation strategies using the MADMAX analysis pipeline pmid:21778530

label: Biotin

source_name: KO-CYP2C70_UDCA Feeding 0.1%_Liver

label_protocol: RNA were processed using Affymetrix GeneChip® WT PLUS Reagent Kit

growth_protocol: Mice were housed in a temperature-controlled room (22–24°C) and 12-hour light/12-hour dark cycles.

extract_protocol: RNA was extracted using nucleosol with cleanup on Mn RNA columns and reverse transcribed using the High Capacity cDNA Reverse Transcription kit (Applied Biosystems, USA). Total RNA was checked for quantity and quality using the Agilent 2100 Bioanalyzer (Agilent Biotechnologies)

treatment_protocol: Total RNA was prepared form Liver tissue of  12 wk old Female mice fed an  0.1% UDCA chow diet for 7wks , starting at the age of 5wks  or a regular  Chow dieet.

tag: strain background

tag: Sex

value: Females

tag: age

tag: diet

value: UDCA Feeding 0.1%

tag: tissue

value: liver


title: SAMPLE 16_WT_Chow

description: RMA - PLM (unlogged scale): 16-m17_(MoGene-2_0-st).CEL (WT)

tag: genotype/variation

value: Chow


title: S13

value: embryo

tag: region

tag: gender

value: Male

tag: embryonic stage

value: 23 somites


title: sequencing of CGA-2-1 gene in HeLa-iCas9-SerCGA sgRNA cells, before iCas9 induction, repeat2

description:
SerCGAsgRNA_d0_CGA-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: cell line

value: HeLa

tag: crispr construct

value: iCas9 - SerCGA sgRNA

tag: icas9 induction

tag: the sequenced trna gene

tag: repeat

value: repeat 2


title: SAMPLE 21_KO-CYP2C70_Chow

description: RMA - PLM (unlogged scale): 21-m22_(MoGene-2_0-st).CEL (KO)


title: SAMPLE 19_WT_UDCA Feeding 0.1%

description: RMA - PLM (unlogged scale): 19-m20_(MoGene-2_0-st).CEL (WT_UDCA)

source_name: WT_UDCA Feeding 0.1%_Liver


title: SAMPLE 18_WT_UDCA Feeding 0.1%

description: RMA - PLM (unlogged scale): 18-m19_(MoGene-2_0-st).CEL (WT_UDCA)


title: SAMPLE 17_WT_Chow

description: RMA - PLM (unlogged scale): 17-m18_(MoGene-2_0-st).CEL (WT)


title: SAMPLE 20_WT_UDCA Feeding 0.1%

description: RMA - PLM (unlogged scale): 20-m21_(MoGene-2_0-st).CEL (WT_UDCA)


title: RNA_Th2_120h_prolong_rep2

tag: strain

tag: cell type

tag: time

tag: differentiation

tag: genotype

value: prolong


title: sequencing of CGA-3-1 gene in HeLa-iCas9-SerCGA sgRNA cells, before iCas9 induction, repeat2

description:
SerCGAsgRNA_d0_CGA-3-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: RNA_Th1KO_96h_rep2

growth_protocol: Splenic CD44low CD62Lhi CD4+ were stimulated under Th1 culture conditions (30 U/ml IL-2 culture sup, 100 U/ml IL-12, and 1 µg/ml anti-IL-4 Ab) in vitro.

value: Cxxc1fl/fl CD4-Cre+

tag: stimulation

tag: in vitro, in vivo


title: S12

tag: tissue

value: Posterior somites

value: Control

value: 24 somites


title: S11

value: Anterior somites


title: RNA_Th1KO_96h_rep1

value: Primary splenic CD4 T cells

value: regular

value: in vitro


title: S7

value: DKO


title: RNA_Th1KO_48h_rep2


title: sequencing of CGA-3-1 gene in HeLa-iCas9-SerCGA sgRNA cells, before iCas9 induction, repeat1

description:
SerCGAsgRNA_d0_CGA-3-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: Day 0


title: RNA_Th1KO_48h_rep1


title: sequencing of CGA-1-1 gene in HeLa-iCas9-SerCGA sgRNA cells, before iCas9 induction, repeat2

description:
SerCGAsgRNA_d0_CGA-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: SAMPLE 15_KO-CYP2C70_UDCA Feeding 0.1%

description: RMA - PLM (unlogged scale): 15-m16_(MoGene-2_0-st).CEL (KO_UDCA)

tag: strain background

tag: genotype/variation

tag: Sex

value: Females

tag: age

tag: diet

value: UDCA Feeding 0.1%

value: liver


title: S5

value: embryo

tag: region

tag: gender

value: Female

tag: embryonic stage

value: 22 somites


title: RNA_Th1_96h_rep2

value: WT


title: RNA_Th1KO_0h_rep1

value: Cxxc1fl/fl CD4-Cre+


title: sequencing of CGG-2-1 gene in HeLa-iCas9-ProCGG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
ProCGGsgRNA_d12_CGG-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

source_name: HeLa iCas9 - ProCGG sgRNA

tag: cell line

value: HeLa

tag: crispr construct

value: iCas9 - ProCGG sgRNA

tag: icas9 induction

value: Day 12

tag: the sequenced trna gene

tag: repeat

value: repeat 2


title: RNA_Th1KO_120h_rep2

tag: strain

tag: cell type

value: Primary splenic CD4 T cells

tag: time

tag: differentiation

tag: genotype


title: S4

tag: tissue

value: Posterior somites

value: Control

value: 20 somites


title: SAMPLE 14_KO-CYP2C70_UDCA Feeding 0.1%

description: RMA - PLM (unlogged scale): 14-m15_(MoGene-2_0-st).CEL (KO_UDCA)

tag: strain background

tag: genotype/variation

tag: Sex


title: S10

tag: region

value: DKO


title: S8

tag: gender

value: Male

value: 24 somites


title: SAMPLE 13_KO-CYP2C70_UDCA Feeding 0.1%

description: RMA - PLM (unlogged scale): 13-m14_(MoGene-2_0-st).CEL (KO_UDCA)

value: Females

tag: age

tag: diet

value: UDCA Feeding 0.1%

value: liver


title: SAMPLE 11_KO-CYP2C70_UDCA Feeding 0.1%

description: RMA - PLM (unlogged scale): 11-m12_(MoGene-2_0-st).CEL (KO_UDCA)


title: sequencing of CGG-1-3 gene in HeLa-iCas9-ProCGG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
ProCGGsgRNA_d12_CGG-1-3_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: cell line

tag: crispr construct


title: S9

value: embryo

value: Anterior somites

value: Female

tag: embryonic stage


title: sequencing of CGA-2-1 gene in HeLa-iCas9-SerCGA sgRNA cells, before iCas9 induction, repeat1

description:
SerCGAsgRNA_d0_CGA-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: HeLa

value: iCas9 - SerCGA sgRNA

tag: icas9 induction

value: Day 0

tag: the sequenced trna gene

tag: repeat


title: sequencing of CGA-1-1 gene in HeLa-iCas9-SerCGA sgRNA cells, before iCas9 induction, repeat1

description:
SerCGAsgRNA_d0_CGA-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: RNA_Th1_96h_prolong_rep2

tag: strain

tag: cell type

tag: time

value: WT

tag: stimulation

value: prolong

tag: in vitro, in vivo

value: in vitro


title: sequencing of CGG-1-3 gene in HeLa-iCas9-ProCGG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
ProCGGsgRNA_d12_CGG-1-3_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: iCas9 - ProCGG sgRNA

value: Day 12


title: S6

tag: tissue

value: Posterior somites

tag: genotype

value: DKO

value: 22 somites


title: RNA_Th1KO_120h_rep1

value: Primary splenic CD4 T cells

tag: differentiation

value: Cxxc1fl/fl CD4-Cre+

value: regular


title: RNA_Th1KO_0h_rep2


title: SAMPLE 8_KO-CYP2C70_Chow

description: RMA - PLM (unlogged scale): 08-m8_(MoGene-2_0-st).CEL (KO)

tag: strain background

tag: genotype/variation

tag: Sex

value: Females

value: Chow

value: liver


title: S2

value: embryo

tag: region

value: Control

tag: gender

value: Female

value: 23 somites


title: RNA_Th1_96h_rep1

value: WT


title: Sample_neuron_P5

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

country: USA

institute: University of Pennsylvania

data_processing:
basecalling: bcl2fastq v1.8.4
Basecalling was done with bcl2fastq versions 1.8.4 and 2.17. Included as a column of the SAMPLES section above, labelled "protocol: basecalling". Reads were trimmed for adapter, low quality base calls, and poly-A sequence using in-house software and then mapped to the mouse genome (mm10) using STAR v2.4.0 (Dobin et al. 2013).
Uniquely mapped reads were used for gene quantification using VERSE v0.1.4 with parameters “-s 1 -z 3 --nonemptyModified” (Zhu et al. 2016, doi:https://doi.org/10.1101/053306)
Genome_build: mm10
Supplementary_files_format_and_content: comma delimited text files containing raw gene counts

source_name: neuron

growth_protocol: Not Applicable

extract_protocol:
We used standard brain slice preparation technology. Briefly, mice were quickly anesthetized in 2% isoflurane, and decapitated. Brains were removed and laced into ice cold artificial cerebrospinal fluid (ACSF). Slices were cut by vibratome (Leica VT1000 S, Leica Biosystems, Wetzlar, Germany) under ice cold ACSF supplied with Carbogen (5% CO2 in 95% oxygen), then were stored in storage ACSF on room temperature in a chamber and permanently supplied by Carbogen for 1 hour before recording. Three hundred µm slices were cut from a mouse brain so that we were able to collect cells from different layers from the prefrontal cortex (PFC). Individual cells were collected by patch-clamp pipette.
libraries made with Illumina TruSeq Stranded kit (RS-122-2101/2)

treatment_protocol: No Treatment

tag: source region

value: cortex

tag: source type

value: acute slice

tag: basecalling

value: bcl2fastq v1.8.4


title: SAMPLE 12_KO-CYP2C70_UDCA Feeding 0.1%

description: RMA - PLM (unlogged scale): 12-m13_(MoGene-2_0-st).CEL (KO_UDCA)

tag: age

tag: diet

value: UDCA Feeding 0.1%


title: RNA_Th1_48h_rep1

tag: strain

tag: cell type

value: in vitro


title: SAMPLE 5_WT_UDCA Feeding 0.1%

description: RMA - PLM (unlogged scale): 05-m5_(MoGene-2_0-st).CEL (WT_UDCA)


title: Sample_neuron_P3


title: sequencing of CGG-1-1 gene in HeLa-iCas9-ProCGG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
ProCGGsgRNA_d12_CGG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

tag: cell line

value: HeLa

tag: crispr construct

value: iCas9 - ProCGG sgRNA

tag: icas9 induction

value: Day 12

tag: the sequenced trna gene

tag: repeat


title: RNA_Th1_48h_prolong_rep1

value: Primary splenic CD4 T cells

tag: time

tag: differentiation

tag: genotype

tag: stimulation

value: prolong

tag: in vitro, in vivo


title: S1

tag: tissue

tag: region

value: Anterior somites

tag: gender

tag: embryonic stage


title: SAMPLE 10_KO-CYP2C70_Chow

description: RMA - PLM (unlogged scale): 10-m10_(MoGene-2_0-st).CEL (KO)

tag: strain background

tag: genotype/variation

tag: Sex

value: Females

tag: age

tag: diet

value: Chow

value: liver


title: SAMPLE 4_WT_UDCA Feeding 0.1%

description: RMA - PLM (unlogged scale): 04-m4_(MoGene-2_0-st).CEL (WT_UDCA)


title: SAMPLE 9_KO-CYP2C70_Chow

description: RMA - PLM (unlogged scale): 09-m9_(MoGene-2_0-st).CEL (KO)


title: SAMPLE 3_WT_Chow

description: RMA - PLM (unlogged scale): 03-m3_(MoGene-2_0-st).CEL (WT)


title: sequencing of CGG-2-1 gene in HeLa-iCas9-ProCGG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
ProCGGsgRNA_d12_CGG-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

tag: cell line

tag: crispr construct

tag: icas9 induction


title: sequencing of CGG-2-1 gene in HeLa-iCas9-ProCGG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
ProCGGsgRNA_d8_CGG-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: Day 8

tag: the sequenced trna gene

tag: repeat


title: Sample_neuron_P1

tag: strain

tag: source region

tag: source type

tag: basecalling


title: RNA_Th1_120h_rep1

tag: cell type

tag: time

tag: differentiation

tag: genotype

tag: stimulation

value: regular

tag: in vitro, in vivo


title: SAMPLE 1_WT_Chow

description: RMA - PLM (unlogged scale): 01-m1_(MoGene-2_0-st).CEL (WT)

tag: strain background

tag: genotype/variation

value: WT

tag: Sex

tag: age

tag: tissue


title: RNA_Th1_120h_rep2


title: RNA_Th1_96h_prolong_rep1


title: S3

value: embryo

tag: region

value: Control

tag: gender

value: Female

tag: embryonic stage

value: 20 somites


title: RNA_Th1_48h_rep2

tag: strain

value: in vitro


title: sequencing of CGG-1-2 gene in HeLa-iCas9-ProCGG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
ProCGGsgRNA_d12_CGG-1-2_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: cell line

value: HeLa

tag: crispr construct

tag: icas9 induction

tag: the sequenced trna gene

tag: repeat

value: repeat 2


title: sequencing of CGG-1-1 gene in HeLa-iCas9-ProCGG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
ProCGGsgRNA_d12_CGG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: iCas9 - ProCGG sgRNA

value: Day 12


title: SAMPLE 6_WT_UDCA Feeding 0.1%

description: RMA - PLM (unlogged scale): 06-m6_(MoGene-2_0-st).CEL (WT_UDCA)

tag: diet

value: UDCA Feeding 0.1%


title: Sample_neuron_F6

tag: source region

value: cortex

tag: source type

value: acute slice

tag: basecalling

value: bcl2fastq v1.8.4


title: SAMPLE 7_KO-CYP2C70_Chow

description: RMA - PLM (unlogged scale): 07-m7_(MoGene-2_0-st).CEL (KO)

tag: strain background

tag: genotype/variation

value: Females

value: Chow

value: liver


title: RNA_Th1_120h_prolong_rep2

tag: cell type

value: Primary splenic CD4 T cells

tag: time

tag: differentiation

tag: genotype

value: WT

tag: stimulation

value: prolong

tag: in vitro, in vivo


title: Sample_neuron_P14

tag: strain


title: Sample_neuron_P2


title: sequencing of CGG-1-2 gene in HeLa-iCas9-ProCGG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
ProCGGsgRNA_d8_CGG-1-2_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: cell line

tag: crispr construct

value: Day 8


title: sequencing of CGG-2-1 gene in HeLa-iCas9-ProCGG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
ProCGGsgRNA_d8_CGG-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: icas9 induction

tag: the sequenced trna gene


title: RNA_Th1_48h_prolong_rep2


title: sequencing of CGG-1-2 gene in HeLa-iCas9-ProCGG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
ProCGGsgRNA_d12_CGG-1-2_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

tag: repeat


title: Sample_neuron_P4

tag: source region


title: sequencing of CGG-1-1 gene in HeLa-iCas9-ProCGG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
ProCGGsgRNA_d8_CGG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: Tumor2-2

city: Nagoya

first: Nishimura

last: Tatsunori

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Graduate School of Medicine

institute: Nagoya University

description: Gene expression of primamary tumor

hyb_protocol: cDNA were subjected to fragmentation and hybridized on SurePrint G3 Human GE ver3.0 8x60K Microarray (Agilent Tech.) following manufacture’s instruction. Then, slides were washed in Agilent Gene Expression Wash Buffers 1 and 2 (Agilent Tech.).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol AgilentG3_GX_1Color and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered wtih two filters with GeneSpring software (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values separately for mouse1 and mouse2 (two tumor and two liver data (in total four data) for each mouse). In the first filter, when the value of a probe was lower than  20 percentile value in all samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was exluded. After flitering, the common probes in mouse1 and mouse 2 were extacted ,and control probes were excluded. Then log scale values were transformed into normal scale, and theprobes of which coefficient of variation was over 0.5 in any four samples (mouse1 tumor, mouse1 liver, mouse2 tumor, mouse2 liver) were omitted. Finally, the probes for whcih the gene symbol were not assigned were also omitted.

source_name: mouse2 tumor

label_protocol: cDNA samples were labeled with cyanine 3-dUTP exploiting SureTag DNA Labeling Kit (Agilent Tech.) according to the manufacturer's instructions/

growth_protocol: Human breast cancer patient-derived xenograft (PDX) mouse model was established by xenotransplantation of the breast cancer tissue into mammary fat pad regions of female immunodeficient NSG mice.

extract_protocol: From the 2,000 sorted PDX cells, total RNA was extracted using RNesy mini kit (Qiagen) according to the manufacturer's instructions. Tehn, cDNA was synthesized and amplified from total RNA exploiting Ovation Pico WTA System V2 (NuGEN).

treatment_protocol: Cancer stem cell marker CD44-positive PDX cells were collected from the PDX tumor at the primary site and the liver of PDX mice using a cell sorter.

tag: marker

value: CD44+ cells

tag: cell tyep

value: PDX cells

tag: sample type

value: primamary tumor


title: sequencing of CGG-1-3 gene in HeLa-iCas9-ProCGG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
ProCGGsgRNA_d8_CGG-1-3_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: HeLa


title: SAMPLE 2_WT_Chow

description: RMA - PLM (unlogged scale): 02-m2_(MoGene-2_0-st).CEL (WT)

tag: strain background

tag: genotype/variation

tag: Sex

tag: age

tag: diet

tag: tissue


title: Liver2-2

description: Gene expression of metastatic tumor

source_name: mouse2 liver

value: metastatic tumor


title: sequencing of CGG-1-2 gene in HeLa-iCas9-ProCGG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
ProCGGsgRNA_d8_CGG-1-2_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: iCas9 - ProCGG sgRNA


title: Sample_neuron_F1

tag: source type

tag: basecalling


title: RNA_Th1_0h_rep2

tag: strain

tag: cell type

tag: time

tag: differentiation

tag: genotype

tag: stimulation

value: regular

tag: in vitro, in vivo

value: in vitro


title: IR+Shh rep1

city: College Station

first: Fei

last: Liu

address: 206 Olsen Blvd

institute: Texas A&M University Health Science Center

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Sequences were aligned to mm10 (GRCm38) using Tophat-2.0.13 alignment software.
The number of reads aligning to genes was counted with Htseq-0.10.0.
Quantification and statistical inference of systematic changes between samples were computed by DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: count file from Htseq in tab deliminated format.

source_name: Adult male 7 days after local IR

extract_protocol:
SMGs were removed, flash frozen on dry ice, and RNA was harvested using Qiagen RNeasy Mini Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: submandibular gland (SMG)

value: male

value: Shh intra-SMG transfer


title: Liver2-1

description: Gene expression of metastatic tumor

tag: marker

tag: cell tyep


title: RNA_Th1_120h_prolong_rep1


title: RNA_Th1_0h_rep1


title: sequencing of CGG-1-3 gene in HeLa-iCas9-ProCGG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
ProCGGsgRNA_d8_CGG-1-3_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: cell line

tag: crispr construct

tag: icas9 induction

tag: the sequenced trna gene

tag: repeat

value: repeat 2


title: Tumor1-2

description: Gene expression of primamary tumor

source_name: mouse1 tumor

tag: sample type


title: ChIP_H3K4Me3_Th2_rep2

tag: chip antibody


title: IR+Shh rep3

tag: tissue

tag: Sex

tag: genotype/variation


title: ChIP_H3K4Me3_Th2_rep1

tag: strain

tag: cell type

tag: time


title: IR+Shh rep2


title: Liver1-2

description: Gene expression of metastatic tumor

source_name: mouse1 liver


title: Tumor2-1

description: Gene expression of primamary tumor


title: ChIP_H3K4Me3_Th2KO_rep2

tag: differentiation

tag: genotype

value: Cxxc1fl/fl CD4-Cre+

tag: stimulation


title: Sample_neuron_F2

tag: source region

value: cortex

tag: source type

value: acute slice

tag: basecalling

value: bcl2fastq v1.8.4


title: ChIP_H3K4Me3_Th2KO_rep1

value: Primary splenic CD4 T cells

tag: in vitro, in vivo


title: sequencing of CGG-2-1 gene in HeLa-iCas9-ProCGG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
ProCGGsgRNA_d4_CGG-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: cell line

tag: crispr construct

tag: icas9 induction

value: Day 4

tag: the sequenced trna gene


title: sequencing of CGG-1-1 gene in HeLa-iCas9-ProCGG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
ProCGGsgRNA_d8_CGG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: Day 8

tag: repeat


title: IR+Gli1 rep1

tag: tissue

tag: Sex

value: Gli1 intra-SMG transfer


title: Liver1-1

description: Gene expression of metastatic tumor

tag: marker

value: CD44+ cells

tag: cell tyep

value: PDX cells

tag: sample type


title: IR+Gli1 rep2

tag: strain

tag: genotype/variation


title: WT_T9_rep2

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

data_processing:
Sequencing reads from RNA-seq were aligned to the mouse reference genome (Version mm10 from UCSC) using Tophat (2.1.0) with default parameters.
The expression values of each gene were quantified as Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) using cufflinks (v2.2.1)
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: footpad skin

growth_protocol: the skin isolate from 8-10 weeks mouse

extract_protocol:
Total RNAs were extracted by using Trizol reagent and standart protocols were followed.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: treat by radition with 5Gy/40Gy

value: footpad skin

tag: treatment

tag: genotype

value: WT

tag: age

value: 8-10 weeks


title: sequencing of CGG-1-3 gene in HeLa-iCas9-ProCGG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
ProCGGsgRNA_d4_CGG-1-3_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: HeLa

value: iCas9 - ProCGG sgRNA


title: Tumor1-1

description: Gene expression of primamary tumor

value: primamary tumor


title: sequencing of CGG-1-2 gene in HeLa-iCas9-ProCGG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
ProCGGsgRNA_d4_CGG-1-2_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: IR+GFP rep1

value: submandibular gland (SMG)

value: male

value: GFP intra-SMG transfer


title: WT_T6_rep1


title: WT_T3_rep2


title: WT_T9_rep1


title: sequencing of CGG-2-1 gene in HeLa-iCas9-ProCGG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
ProCGGsgRNA_d4_CGG-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: ChIP_H3K4Me3_input

tag: cell type

tag: time

tag: differentiation

tag: stimulation

value: regular

value: in vitro

tag: chip antibody


title: ChIP_H3K4Me3_Th1KO_rep2

value: Primary splenic CD4 T cells

value: Cxxc1fl/fl CD4-Cre+

tag: in vitro, in vivo


title: ChIP_Cxxc1_Flag_Th2_rep2

value: Anti-Flag


title: WT_T6_rep2


title: IR+GFP rep2


title: IR+GFP rep3


title: ChIP_H3K4Me3_Th1_rep1


title: sequencing of CGG-1-2 gene in HeLa-iCas9-ProCGG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
ProCGGsgRNA_d4_CGG-1-2_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: cell line

tag: crispr construct

tag: icas9 induction

value: Day 4

tag: the sequenced trna gene

tag: repeat

value: repeat 2


title: ChIP_H3K4Me3_Th1KO_rep1


title: ChIP_H3K4Me3_Th1_rep2


title: IR+Gli1 rep3

tag: tissue

tag: Sex

value: Gli1 intra-SMG transfer


title: ChIP_Cxxc1_Flag_Th2_rep1

tag: strain


title: sequencing of CGG-1-1 gene in HeLa-iCas9-ProCGG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
ProCGGsgRNA_d4_CGG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: WT_T3_rep1

value: footpad skin

tag: treatment


title: sequencing of CGG-1-3 gene in HeLa-iCas9-ProCGG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
ProCGGsgRNA_d4_CGG-1-3_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: IR rep1

tag: genotype/variation

value: wild type


title: K17_T9_rep2

tag: genotype

value: Krt17 Knock out

tag: age

value: 8-10 weeks


title: IR rep3


title: sequencing of CGG-2-1 gene in HeLa-iCas9-ProCGG sgRNA cells, before iCas9 induction, repeat1

description:
ProCGGsgRNA_d0_CGG-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: HeLa

value: iCas9 - ProCGG sgRNA

value: Day 0


title: sequencing of CGG-2-1 gene in HeLa-iCas9-ProCGG sgRNA cells, before iCas9 induction, repeat2

description:
ProCGGsgRNA_d0_CGG-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: sequencing of CGG-1-1 gene in HeLa-iCas9-ProCGG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
ProCGGsgRNA_d4_CGG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: sequencing of CGG-1-3 gene in HeLa-iCas9-ProCGG sgRNA cells, before iCas9 induction, repeat2

description:
ProCGGsgRNA_d0_CGG-1-3_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: IR rep2

value: submandibular gland (SMG)

value: male


title: ChIP_Cxxc1_Flag_Th1_rep2

tag: cell type

tag: time

value: WT

value: regular


title: NT rep3

source_name: Adult male non-treated


title: K17_T9_rep1


title: WT_T0_rep2

value: Control


title: WT_T0_rep1


title: NT rep2


title: sequencing of CGG-1-3 gene in HeLa-iCas9-ProCGG sgRNA cells, before iCas9 induction, repeat1

description:
ProCGGsgRNA_d0_CGG-1-3_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: K17_T6_rep1


title: WT_H3K9me3_ChIPSeq_input.fq.gz

city: Tianjin

first: Yajing

last: Chu

address: Nanjing Road 288

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology, Chinese Academy of Medical Sciences

description:
input DNA
cell purification protocol : c-Kit+ cells were isolated with CD117 beads from bone marrow of wild-type and moribund leukemic mice according to the protocol (Miltenyi, Bergisch Gladbach, Germany)

data_processing:
Raw image data file from high-throughput sequencing (Illumina HiSeqTM) was transformed to Raw Data by CASAVA 1.8 base recognition (Base Calling)
Raw reads were filtered ausing fastx (version:0.0.13,http://hannonlab.cshl.edu/fastx_toolkit/index.html )
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie (version:0.12.8)
peaks were called using MACS (version:1.4.2).
Genome_build: mm10
Supplementary_files_format_and_content: wig files for each samples (visualized in IGV tools)

source_name: WT c-Kit+ hematopoietic cells from bone marrow

extract_protocol:
ChIPed DNA or input DNA was isolated from the enriched c-Kit+ cells following standard protocol with phenol chloroform reagent (Sigma).
Libraries were prepared according to Illumina's TruSeq® ChIP Sample Preparation following the manufacturer's protocols.

value: bone marrow

tag: mouse model

value: wildtype mice

tag: overexpression


title: K17_T6_rep2


title: ChIP_Cxxc1_Flag_input

source_name: Primary splenic CD4 T cells

value: Primary splenic CD4 T cells

tag: differentiation

tag: stimulation

tag: in vitro, in vivo

value: in vitro

tag: chip antibody


title: sequencing of CGG-1-2 gene in HeLa-iCas9-ProCGG sgRNA cells, before iCas9 induction, repeat2

description:
ProCGGsgRNA_d0_CGG-1-2_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: cell line

tag: crispr construct

tag: icas9 induction

tag: the sequenced trna gene

value: repeat 2


title: sequencing of CGG-1-2 gene in HeLa-iCas9-ProCGG sgRNA cells, before iCas9 induction, repeat1

description:
ProCGGsgRNA_d0_CGG-1-2_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

tag: repeat


title: K17_T3_rep2

tag: tissue

value: footpad skin

tag: treatment


title: NT rep1

tag: strain

tag: Sex

tag: genotype/variation

value: wild type


title: K17_T3_rep1

tag: genotype

value: Krt17 Knock out

tag: age


title: ATAC_Th2_96h_rep1

tag: cell type

tag: time


title: MN3_H3K9me3_ChIPSeq_input.fq.gz

source_name: MN3 c-Kit+ leukemic cells from bone marrow

tag: mouse model

value: MLL-NRIP3 induce acute myeloid leukemia

tag: overexpression


title: ATAC_Th2_96h_Cxxc1KO_rep1

tag: differentiation

value: Cxxc1fl/fl CD4-Cre+

tag: stimulation

tag: in vitro, in vivo


title: K17_T0_rep2

value: 8-10 weeks


title: sequencing of CGG-1-1 gene in HeLa-iCas9-ProCGG sgRNA cells, before iCas9 induction, repeat1

description:
ProCGGsgRNA_d0_CGG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

tag: cell line

value: HeLa

tag: crispr construct

value: iCas9 - ProCGG sgRNA

tag: icas9 induction

value: Day 0


title: MA9_H3K9me3_ChIPSeq_2_input.fq.gz

source_name: MA9 c-Kit+ leukemic cells from bone marrow

tag: tissue

value: MLL-AF9 induce acute myeloid leukemia


title: sequencing of TAG-3-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d12_TAG-3-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

source_name: HeLa iCas9 - LeuTAG sgRNA

value: iCas9 - LeuTAG sgRNA

value: Day 12

tag: the sequenced trna gene

tag: repeat


title: sequencing of TAG-2-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d12_TAG-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: ATAC_Th2_72h_rep2

tag: strain

value: WT

value: regular


title: ATAC_Th2_96h_Cxxc1KO_rep2

value: Primary splenic CD4 T cells


title: sequencing of TAG-3-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d12_TAG-3-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: ATAC_Th2_72h_rep1

value: in vitro


title: MN3_H3K9me3_ChIPSeq.fq.gz

description:
H3K9me3 ChIPed DNA
cell purification protocol : c-Kit+ cells were isolated with CD117 beads from bone marrow of wild-type and moribund leukemic mice according to the protocol (Miltenyi, Bergisch Gladbach, Germany)

value: bone marrow

tag: chip antibody


title: sequencing of TAG-2-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d12_TAG-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: sequencing of CGG-1-1 gene in HeLa-iCas9-ProCGG sgRNA cells, before iCas9 induction, repeat2

description:
ProCGGsgRNA_d0_CGG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: repeat 2


title: K17_T0_rep1

value: footpad skin

tag: treatment

value: Control

tag: genotype


title: p53_6h_rep2

source_name: back skin hair in growth phase

value: back skin

value: p53 Knock out

tag: age


title: p53_24h_rep2

value: 8-10 weeks


title: MA9_H3K9me3_ChIPSeq_2.fq.gz


title: ATAC_Th2_96h_rep2

tag: cell type

tag: time


title: p53_24h_rep1


title: ATAC_Th2_72h_Cxxc1KO_rep2

value: Cxxc1fl/fl CD4-Cre+


title: MA9_H3K9me3_ChIPSeq_1_input.fq.gz

tag: mouse model

tag: overexpression


title: WT_H3K9me3_ChIPSeq.fq.gz

value: wildtype mice


title: p53_6h_rep1


title: p53_0h_rep2


title: MA9_H3K9me3_ChIPSeq_1.fq.gz


title: EKO/hA-I Western Diet 22 weeks rep 3

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads were mapped on the GencodeM annotation of the Mus musculus transcriptome using the bowtie2 program. Estimation of gene expression levels was performed using RSEM. Differential expression analysis was performed applying the quasilikelihood (QL) F-test of the edgeR38 package to RSEM estimated reads counts. Only genes with more than 10 reads in at least 4 different biological replicates were considered. Genes showing a false discovery rate lower than 0.05 were considered differentially expressed
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Aorta

growth_protocol: Eight weeks old mice were randomly divided into 4 groups of 8 mice and fed a regular chow diet (4RF21, Mucedola, Italy) or a Western diet (TD.88137, Envigo, Italy) for 6 or 22 weeks. One week before the end of the dietary treatment, after an overnight fast, mice were anaesthetized with 2% isoflurane (Merial Animal Health, Woking, UK). Blood was collected from the retroorbital plexus into tubes containing 0.1% (w/v) EDTA and centrifuged in a microcentrifuge for 10 minutes at 5900 × g at 4 °C. At the end of the dietary treatments, mice were sacrificed under general anaesthesia with 2% isoflurane (Merial Animal Health, Woking, UK) and blood was removed by perfusion with 1× phosphate-buffered saline (PBS).

extract_protocol:
The aorta was rapidly dissected from the aortic root to the iliac bifurcation and periadventitial fat was removed. Aortas were then snap-frozen in liquid nitrogen for RNA-seq analyses (n=3).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: aorta

value: post natal week 30

value: EKO/hA-I


title: sequencing of TAG-1-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d12_TAG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: HeLa

value: iCas9 - LeuTAG sgRNA

value: Day 12


title: EKO/hA-I Western Diet 22 weeks rep 2


title: p53_0h_rep1


title: ATAC_Th2_96h_APC

value: Primary splenic CD4 T cells

tag: differentiation

value: WT

tag: stimulation

value: regular


title: EKO/hA-I Western Diet 22 weeks rep 1


title: ATAC_Th2_48h_rep2

tag: in vitro, in vivo

value: in vitro


title: sequencing of TAG-3-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d8_TAG-3-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

tag: cell line

tag: crispr construct

value: Day 8


title: EKO/hA-I Western Diet 6 weeks rep 3

tag: tissue

value: post natal week 14


title: ATAC_Th2_48h_rep1


title: sequencing of TAG-2-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d8_TAG-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: icas9 induction

tag: the sequenced trna gene

value: repeat 2


title: WT_24h_rep1

value: back skin


title: ATAC_Th2_48h_Cxxc1KO_rep2

tag: strain


title: EKO/hA-I Western Diet 6 weeks rep 2


title: ATAC_Th2_72h_APC


title: ATAC_Th2_72h_Cxxc1KO_rep1


title: sequencing of TAG-1-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d12_TAG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: repeat


title: EKO/hA-I Western Diet 6 weeks rep 1


title: ATAC_Th2_48h_APC


title: WT_6h_rep2

tag: treatment

value: 8-10 weeks


title: ATAC_Th2_48h_Cxxc1KO_rep1

tag: genotype

value: Cxxc1fl/fl CD4-Cre+


title: sequencing of TAG-1-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d8_TAG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: EKO/hA-I chow 22 weeks rep 3

tag: age


title: ATAC_Th2_24h_rep2

tag: cell type


title: sequencing of TAG-3-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d8_TAG-3-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: WT_24h_rep2


title: WT_0h_rep2

value: Control


title: sequencing of TAG-3-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d4_TAG-3-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: Day 4


title: sequencing of TAG-2-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d8_TAG-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: EKO/hA-I chow 22 weeks rep 2

value: aorta

value: post natal week 30


title: ATAC_Th2_24h_rep1

tag: time


title: EKO/hA-I chow 22 weeks rep 1

value: EKO/hA-I


title: ATAC_Th2_24h_Cxxc1KO_rep2


title: EKO/hA-I chow 6 weeks rep 2


title: K17_24h_rep2

value: Krt17 Knock out


title: K17_24h_rep1


title: ChIP_Cxxc1_Flag_Th1_rep1

tag: chip antibody

value: Anti-Flag


title: WT_6h_rep1


title: ATAC_Th2_24h_Cxxc1KO_rep1

value: Primary splenic CD4 T cells


title: sequencing of TAG-3-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d4_TAG-3-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: HeLa

value: iCas9 - LeuTAG sgRNA


title: sequencing of TAG-2-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d4_TAG-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: EKO/hA-I chow 6 weeks rep 1


title: sequencing of TAG-2-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d4_TAG-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: K17_6h_rep1


title: ATAC_Th2_120h_rep2

value: WT

value: regular

value: in vitro


title: ATAC_Th2_24h_APC


title: sequencing of TAG-1-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d8_TAG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: Day 8


title: WT_0h_rep1

value: back skin


title: sequencing of TAG-1-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d4_TAG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: sequencing of TAG-3-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, before iCas9 induction, repeat2

description:
LeuTAGsgRNA_d0_TAG-3-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: Day 0

value: repeat 2


title: sequencing of TAG-2-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, before iCas9 induction, repeat2

description:
LeuTAGsgRNA_d0_TAG-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: sequencing of TAG-3-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, before iCas9 induction, repeat1

description:
LeuTAGsgRNA_d0_TAG-3-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: K17_0h_rep2

value: Control

value: 8-10 weeks


title: ATAC_Th2_120h_Cxxc1KO_rep1

value: Cxxc1fl/fl CD4-Cre+


title: RNASeq_D2_siKctd10 #3

city: Berkeley

first: Michael

last: Rape

state: CA

address: 1951 Oxford St Li Ka Shing Center, 330A

institute: University of California, Berkeley

data_processing:
For RNAseq samples, reads were aligned to transcripts with HISAT under the following parameters (Hisat -5 35 -3 35 -p 7 -x mm10.idx -S <filename.sam> -1 R1.fastq.gz -2 R2.fastq.gz). SAM files were sorted using samtools
sorted.BAM files were mapped using stringtie (1.1.3) using following parameters (stringtie <filename.sorted.bam> -o <filename.gtf> -G mm10.gtf -eB -p 7
Stringtie .gtf files were then processed using the Python scirpt prepDE (see StringTie documentation) and analyzed using DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: GTF (General Transfer format) are presented. Values  contain transcript names (UCSC Gene IDs), transcirpt lengths, FPKMs, and TPMs

growth_protocol:
For samples FRP1-FRP6, C2C12s were grown subconfluenly in DMEM+10%FBS
For samples FRP7-FRP12, C2C12s were switched to differentiation media (DMEM + 2% Horse Serum) 24 h after treatment with siRNAs. Cells were kept in DM until day of harvesting

extract_protocol:
All cellular samples were harvested using ice-cold PBS and pelleted.
Total RNA was extracted from differntiating myocyte C2C12s treated with siControl or siKctd10  or siCNTRL siRNAs (in triplicate) using a NucleoSpin Plus RNA extraction kit (Machery-  Nagel)
Total RNA was polyA selected, end-repaired, adaptor ligated, and PCR amplified with desired indeces

treatment_protocol: C2C12s were treated with indicated siRNAs, switched to differentiaiton media (DMEM + 2% Horse Serum) 24 h after depletion, and harvested 48 h after initial differentiation

value: Differentiating myocyte (D2)

tag: knockdown


title: RNASeq_D2_siKctd10 #2


title: K17_6h_rep2


title: ATAC_Th2_120h_Cxxc1KO_rep2

tag: differentiation


title: ATAC_Th2_120h_APC

tag: stimulation


title: sequencing of TAG-2-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, before iCas9 induction, repeat1

description:
LeuTAGsgRNA_d0_TAG-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: sequencing of TAG-1-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, before iCas9 induction, repeat2

description:
LeuTAGsgRNA_d0_TAG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: ATAC_Th1_96h_rep2

tag: in vitro, in vivo


title: RNASeq_D2_siKctd10 #1


title: ATAC_Th2_120h_rep1


title: ATAC_Th1_96h_Cxxc1KO_rep2


title: RNASeq_D2_siCont #1

value: siControl


title: sequencing of TCG-6-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d12_TCG-6-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

source_name: HeLa iCas9 - ArgTCG sgRNA

tag: cell line

value: iCas9 - ArgTCG sgRNA

value: Day 12


title: ATAC_Th1_96h_Cxxc1KO_rep1

value: Primary splenic CD4 T cells


title: ATAC_Th1_96h_rep1


title: sequencing of TAG-1-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d4_TAG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: HeLa

tag: crispr construct

value: Day 4


title: RNASeq_D2_siCont #2


title: sequencing of TAG-1-1 gene in HeLa-iCas9-LeuTAG sgRNA cells, before iCas9 induction, repeat1

description:
LeuTAGsgRNA_d0_TAG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: iCas9 - LeuTAG sgRNA


title: ATAC_Th1_96h_APC

value: WT

value: regular


title: sequencing of TCG-6-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d12_TCG-6-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: RNASeq_D0_siKctd10 #3

extract_protocol:
All cellular samples were harvested using ice-cold PBS and pelleted.
Total RNA was extracted from sub-confluent C2C12s treated with siControl or siKctd10  or siCNTRL siRNAs (in triplicate) using a NucleoSpin Plus RNA extraction kit (Machery-  Nagel)
Total RNA was polyA selected, end-repaired, adaptor ligated, and PCR amplified with desired indeces

treatment_protocol: C2C12s were treated with indicated siRNAs for 48 hrs before harvesting and RNA extraction

value: undifferentiated myoblast


title: RNASeq_D0_siKctd10 #2


title: RNASeq_D2_siCont #3


title: RNASeq_D0_siKctd10 #1


title: ATAC_Th1_72h_Cxxc1KO_rep2

value: in vitro


title: K17_0h_rep1

tag: tissue

value: back skin

value: Krt17 Knock out


title: ATAC_Th1_72h_rep1


title: RNASeq_D0_siCont #2


title: WT Western Diet 22 weeks rep 1

value: aorta

value: post natal week 30

value: wild type


title: ATAC_Th1_72h_Cxxc1KO_rep1

value: Cxxc1fl/fl CD4-Cre+


title: WT Western Diet 22 weeks rep 2


title: RNASeq_D0_siCont #3

value: siControl


title: ATAC_Th1_72h_APC


title: RNASeq_D0_siCont #1


title: sequencing of TCG-3-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d12_TCG-3-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: iCas9 - ArgTCG sgRNA

tag: icas9 induction


title: sequencing of TCG-5-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d12_TCG-5-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: Day 12

tag: the sequenced trna gene

value: repeat 2


title: WT Western Diet 6 weeks rep 2

tag: strain

value: post natal week 14


title: WT Western Diet 6 weeks rep 3


title: ATAC_Th1_48h_rep2

value: Primary splenic CD4 T cells


title: control_3_rnaseq

city: San Francisco

first: Robert

last: Blelloch

state: California

address: 35 Medical Center Way

department: Dept. of Urology

institute: UC, San Francisco

description: untreated controls

data_processing:
Reads were first trimmed for illumina adapters with Cutadapt version 2.5 and then mapped to the mouse mm10 genome using STAR version 2.5.3a in single-end mode
Following alignment, reads were counted using featureCount version 1.6.4.
We then performed differential gene expression analysis using the DESeq2 package version 1.24 and R version 3.6.1.
Genome_build: mm10
Supplementary_files_format_and_content: Exon counts from featureCounts compiled into a .csv file
Supplementary_files_format_and_content: DESeq2 results for all genes comparing bNGF to control samples

source_name: tibial fracture callus-derived hypertrophic cartilage

growth_protocol: Cartilage explants were isolated from the central portion of the day 7 fracture callus using a dissecting microscope to remove any adherent non- cartilaginous tissues and the perichondrium. Explants were minced, pooled, then separated randomly into 2 treatment groups. Explants were grown in vitro for 1 week in serum-free hypertrophic chondrogenic medium to promote hypertrophic maturation

extract_protocol:
Samples were collected in Trizol, then mRNA was extracted using RNeasy Mini Kit following the manufacturer’s instructions (Qiagen cat# 74104). After mRNA extraction from hypertrophic cartilage, samples were then further purified by sodium acetate and isopropanol precipitation.
200ng RNA input from each sample was used with Quantseq 3’ mRNA-seq Library Prep Kit FWD (Lexogen, SKU:015.24) following manufacturers guidelines. Library quality and concentration was determined by Agilent Tapestation 4200 using High Sensitivity D1000 reagents (Agilent, 5067-5603, 5067-5584).

treatment_protocol: Hypertrophic cartilage explants were stimulated with or without 200ng/mL recombinant human β-NGF (Peprotech cat# 450-01) for 24 hours

tag: Stage

value: 7d post fracture, 7d in culture

value: Untreated


title: sequencing of TCG-2-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d12_TCG-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: HeLa

tag: repeat


title: sequencing of TCG-3-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d12_TCG-3-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: sequencing of TCG-4-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d12_TCG-4-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: control_2_rnaseq

description: untreated controls

value: tibial fracture callus-derived hypertrophic cartilage

tag: treatment


title: sequencing of TCG-4-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d12_TCG-4-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: WT Western Diet 22 weeks rep 3

tag: age

tag: genotype

value: EKO


title: ATAC_Th1_72h_rep2

tag: cell type

tag: time

value: WT

value: regular

value: in vitro


title: WT Western Diet 6 weeks rep 1

value: aorta


title: ATAC_Th1_48h_Cxxc1KO_rep2


title: sequencing of TCG-2-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d12_TCG-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: sequencing of TCG-5-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d12_TCG-5-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: WT chow 22 weeks rep 3

value: post natal week 30

value: wild type


title: control_1_rnaseq

description: untreated controls


title: bNGF_4_rnaseq

description: Treated 24h with 200ng/mL recombinant human β-NGF

value: Treated 24hr with bNGF


title: ATAC_Th1_48h_Cxxc1KO_rep1

value: Cxxc1fl/fl CD4-Cre+


title: sequencing of TCG-1-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d12_TCG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: iCas9 - ArgTCG sgRNA

value: Day 12


title: bNGF_2_rnaseq


title: ATAC_Th1_48h_APC


title: sequencing of TCG-1-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d12_TCG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: sequencing of TCG-6-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d8_TCG-6-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: Day 8

value: repeat 2


title: ATAC_Th1_24h_rep2

value: Primary splenic CD4 T cells


title: WT chow 6 weeks rep 3

value: post natal week 14


title: WT chow 22 weeks rep 1


title: WT chow 6 weeks rep 2


title: ATAC_Th1_24h_rep1


title: 94703_RC9_2iL_2

city: Cologne

first: Andreas

last: Beyer

address: Joseph-Stelzmann-Str. 26

department: CECAD

country: Germany

institute: University of Cologne

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv

data_processing:
STAR (version 2.5.3) was used to align single end reads and to retrieve raw counts
STAR(version 2.5.2b) was used to align paired end reads and to retrieve raw counts
FPKM values were calculated using DeSEQ2 (version 1.20.0).
TPM values were calculated using exon sizes from gencode.vM11.primary_assembly.annotation.gtf
Genome_build: mm10
Supplementary_files_format_and_content: CSV (raw counts of single and paired end data in separate files; FPKM of single end data; TPM of paired end data)

source_name: embryonic stem cells

growth_protocol: Cells were maintained in DMEM supplemented with 15% FCS (batch tested, Biowest), 1x Penicillin-Streptomycin (Sigma), 0.1mM NEEA, 1mM sodium pyruvate, 1mM L-glutamine, 0.05mM 2-mercatpoethanol (Gibco), 10ng/mL LIF (batch tested, in-house), 1.5µM CHIRON and 0.5µM PD0325901 (ESDMEM-2i) on gelatin coated plates.

extract_protocol:
RNA was extraced with the RNeasy Mini Kit (Qiagen) according to the manufacturer`s protocol.
[1] Single end data: mRNA was isolated from 1 ug total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s instructions. Final elution was done in 15ul 2x first strand cDNA synthesis buffer (NEBnext, NEB). After chemical fragmentation by incubating for 15 min at 94°C the sample was directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB). For ligation custom adaptors were used 1: (Adaptor-Oligo 5'-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT-3', Adaptor-Oligo 2: 5'-P-GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CAC-3'). After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding beads in a ratio of 1:1, followed by an index PCR (15 cycles) using Illumina compatible index primer. After double XP beads purifications (with beads added in a ratio 1:1) libraries were quantified on a Fragment Analyzer run with a NGS Assay Kit (Agilent) and loaded on a HiSeq 3000 flowcell with 50 cycles single end seqeuncing by pooling the samples in respect of their molarity aiming at 30 mio. reads per sample.
[2] paired-end data: Illumina TruSeq mRNA stranded

treatment_protocol: Differentiation medium (N2B27) consisted of a 1:1 mixture of DMEM/F12 and Neurobasal medium supplemented with 1x B27 (Gibco), 0.5x N2 (homemade), 0.1mM NEAA, 1mM L-glutamine, 1x Penicillin-Streptomycin and 0.05mM 2-mercaptoethanol. 24h before starting differentiation, medium was changed from maintenance ESDMEM-2i medium to N2B27 medium supplemented with 3µM CHIR99201 and 1µM PD0325901 (N2B27-2i). Cells were differentiated in parallel in duplicates for 2-32 hours in unsupplemented N2B27. The undifferentiated control samples were cultured in N2B27-2i.

tag: medium

value: 2i LIF

tag: time point

value: 0 h


title: sequencing of TCG-5-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d8_TCG-5-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: HeLa


title: sequencing of TCG-6-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d8_TCG-6-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: WT chow 6 weeks rep 1


title: ATAC_Th1_24h_Cxxc1KO_rep2

tag: differentiation

tag: stimulation


title: sequencing of TCG-5-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d8_TCG-5-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

tag: cell line


title: ATAC_Th1_48h_rep1

value: WT

tag: in vitro, in vivo


title: PKNP3

city: New Delhi

first: Rita

last: Sharma

state: Delhi

address: SCIS, JNU

department: School of Computational & Integrative Sciences

country: India

institute: Jawaharlal Nehru University

description: Transcriptome

data_processing:
Low-quality reads with Phred score<30 were filtered
NGSQC Toolkit for qulity filtering of the reads
read alignment to the genome using Hisat (2.1.0 )
estimation of gene expression and transcript abundance using StringTie (1.3.3b)
pairwise differential expression analysis using cuffdiff
Genome_build: MSU database
Supplementary_files_format_and_content: FPKM values in excel format

organism: Oryza sativa

source_name: Peduncle

growth_protocol: Oryza sativa plants were raised in an open field

extract_protocol:
Total RNA was isolated using a modified trizol method
Libraries were prepared using TruSeq® Stranded Total RNA kit using manufacturer’s instructions

tag: tissue

value: First Internode

tag: developmental stage

value: Non-elongating peduncle After heading


title: 94699_RC9_2i_2

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv


title: ATAC_Th1_24h_Cxxc1KO_rep1

extract_protocol:
ATAC-seq; Fifty thousand cells were pelleted and washed with 50 μl of 1× PBS, followed by treatment with 50 μl of lysis buffer. The nuclei were re-suspended in 40 μl of TDE buffer with 2 μl of Tn5 transposase (15027865, 15027866; Illumina) to tag and fragmentize the accessible chromatin. The reaction was incubated at 37°C with shaking at 300 rpm for 30 minutes. The fragmentized DNAs were purified using a QIAGEN MinElute kit and amplified with 11 or 12 PCR cycles, based on the amplification curve. ChIP-seq; 1–10×10e6 cells were fixed with 1% paraformaldehyde at 37°C for 10 min. Cells were sedimented, washed, and lysed with SDS lysis buffer (50 mM Tris-HCl, 1% SDS, 10 mM EDTA, 1 mM PMSF, 1 mg/ml aprotinin, and 1 mg/ml leupeptin). The lysates were sonicated to reduce the DNA lengths to between 200 and 1000 bps. The soluble fraction was diluted in ChIP dilution buffer and incubated with Ab conjugated with Dynabeads protein A and G overnight at 4°C. The immune complexes were then captured using a magnet and washed with low-salt, high-salt, LiCl, and Tris–EDTA wash buffer. Enriched chromatin fragments were eluted with elution buffer (0.1 M NaHCO3 containing 1% SDS). The eluted material was incubated at 65°C for 6 h to reverse the formaldehyde cross-links and treated with RNase A (10 mg/ml) and Proteinase K (40 mg/ml). DNA was extracted with a QIAquick PCR purification kit (QIAGEN). RNA-seq; Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
ATAC-seq; The libraries were sequenced for 50 cycles (paired-end reads) on an Illumina HiSeq 1500. ChIP-seq; Ab-specific immunoprecipitates and total input DNA samples were prepared using a SMARTer ThruPLEX DNA-Seq Kit (TaKaRa). RNA-seq; TruSeq Stranded mRNA Library Preparation Kit (Illumina) was used according to the manufacturer's protocol.

value: regular

value: in vitro


title: PKNP2

description: Transcriptome


title: 94697_RC9_2i_1

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv


title: sequencing of TCG-4-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d8_TCG-4-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: crispr construct

tag: icas9 induction

tag: the sequenced trna gene


title: ATAC_Th1_24h_APC

tag: strain


title: WT chow 22 weeks rep 2

value: aorta

value: post natal week 30

value: wild type


title: bNGF_1_rnaseq

value: tibial fracture callus-derived hypertrophic cartilage

tag: Stage

value: 7d post fracture, 7d in culture

tag: treatment

value: Treated 24hr with bNGF


title: ATAC_Th1_120h_rep2

tag: genotype


title: sequencing of TCG-3-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d8_TCG-3-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: iCas9 - ArgTCG sgRNA

value: Day 8

tag: repeat

value: repeat 2


title: 94695_RC9_32h_2

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv


title: 94693_RC9_32h_1

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv


title: ATAC_Th1_120h_rep1

tag: cell type

value: Primary splenic CD4 T cells

tag: time


title: sequencing of TCG-4-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d8_TCG-4-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: 94701_RC9_2iL_1

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv

tag: medium

value: 2i LIF

tag: time point

value: 0 h


title: PKNP1

description: Transcriptome


title: sequencing of TCG-3-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d8_TCG-3-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: HeLa


title: PKEP3

description: Transcriptome

value: First Internode

value: Elongating peduncle Before heading


title: ATAC_Th1_120h_Cxxc1KO_rep2

tag: differentiation

value: Cxxc1fl/fl CD4-Cre+

tag: stimulation

value: regular


title: PKEP1

description: Transcriptome


title: ATAC_Th1_120h_Cxxc1KO_rep1

tag: in vitro, in vivo

value: in vitro


title: 94689_RC9_28h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv


title: sequencing of TCG-2-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d8_TCG-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: cell line


title: ATAC_Th1_120h_APC

value: WT


title: 94691_RC9_30h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv


title: 94687_RC9_26h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv


title: 94685_RC9_24h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv


title: sequencing of TCG-1-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d8_TCG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: sequencing of TCG-1-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d8_TCG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: SWNP3

description: Transcriptome

tag: tissue

tag: developmental stage

value: Non-elongating peduncle After haeding


title: SWNP1

description: Transcriptome

value: Non-elongating peduncle After heading


title: ATAC_Lung_Cxxc1WT_rep1

source_name: Pulmonary CD4 T cells

growth_protocol: Pulmonary CD44hi CD4+ cells were sorted by cell sorter.

value: Pulmonary CD4 T cells

value: in vivo


title: ATAC_Lung_Cxxc1WT_rep2


title: sequencing of TCG-6-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d4_TCG-6-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: crispr construct

value: iCas9 - ArgTCG sgRNA

tag: icas9 induction

value: Day 4


title: 94683_RC9_22h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv

tag: strain


title: 94681_RC9_20h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv


title: ATAC_Lung_Cxxc1KO_rep2


title: SWEP3

description: Transcriptome


title: PKEP2

description: Transcriptome


title: sequencing of TCG-6-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d4_TCG-6-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

tag: the sequenced trna gene


title: 94679_RC9_18h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv


title: ATAC_0h_rep2


title: ATAC_Lung_Cxxc1KO_rep1


title: 94675_RC9_14h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv


title: sequencing of TCG-4-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d4_TCG-4-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: repeat 2


title: SWEP2

description: Transcriptome


title: SWEP1

description: Transcriptome


title: sequencing of TCG-2-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d8_TCG-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

value: Day 8


title: ATAC_0h_Cxxc1KO_rep1

value: Primary splenic CD4 T cells


title: 94669_RC9_8h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv

value: 8 h


title: sequencing of TCG-5-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d4_TCG-5-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: HeLa


title: ATAC_0h_APC


title: 94677_RC9_16h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv


title: ATAC_0h_rep1


title: ATAC_0h_Cxxc1KO_rep2


title: SWNP2

description: Transcriptome

value: First Internode


title: 94673_RC9_12h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv


title: 94665_RC9_4h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv

value: 4 h


title: sequencing of TCG-5-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d4_TCG-5-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: sequencing of TCG-4-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d4_TCG-4-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: sequencing of TCG-3-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d4_TCG-3-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: 94663_RC9_2h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv

value: 2 h


title: 94667_RC9_6h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv

value: 6 h


title: E2 B3 d21 BAL

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: d21 M.tuberculosis BAL sample

hyb_protocol: Whole mouse genome 8x60K microarray hybridizations and washing were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting and 20bit image depth with 3 x 3 micron  pixel resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1. (Agilent) using default parameters (protocol GE1_1105_Oct12) to obtain background subtracted and spatially detrended Processed Signal intensities. Background correction ( normexp) and normalization between arrays  (quantile). Control probe removed.

source_name: BAL

label_protocol: RNA labeling was performed with the low input Quick Amp Labeling Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: For BAL collection, mice were lethally anesthetized.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol using Glycogen as carrier.

treatment_protocol: The bronchoalveolar space was flushed with 1ml of PBS containing protease inhibitor cocktail (Roche). Cells were pelleted and the supernatant sterilized by filtration (0.22 µm) and frozen at -20°C for protein analyses. Subsequently, the alveolar space was flushed 3 additional times with 1ml PBS containing 5 mM EDTA and collected on ice. Cells were pelleted and supernatant discarded. Cells from all washes were combined and kept on ice until further use.

tag: experiment

value: exp 2

tag: treatment

value: day 21


title: sequencing of TCG-3-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d4_TCG-3-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

tag: repeat


title: sequencing of TCG-2-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d4_TCG-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: 94671_RC9_10h

description:
[2]
counts_2hrTC.csv
TPM_2hrTC.csv

tag: genotype


title: sequencing of TCG-1-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_d4_TCG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: EZH2 K735R_RNAseq_rep2

city: Shanghai

first: Huairui

last: Yuan

address: 320 Yueyang Road

department: Shanghai Institutes for Biological Sciences

institute: Chinese Academy of Sciences

data_processing:
For RNA-Seq, transcriptome reads from Hiseq RNA-Seq experiments were mapped to the reference genome (mm10) by using Bowtie tool. Gene expression levels were quantified by a software package called RSEM. The list of significance was operated by setting fold changes threshold at level of 1.5 and p value < 0.05.
Genome_build: mm10

source_name: organoid cells

growth_protocol: The mouse prostatic organoid cells generation and organoids formation assay were according to previously reported protocol (Drost et al., 2016).

extract_protocol:
Total RNA was extracted from the prostatic organoid cells derived from 2-month-old PtenPC-/- and PtenPC-/-; Ezh2K735R mice, and then subjected to PE150 Hiseq.
Libraries were prepared according to standard Illumina protocols.

tag: cell type

value: Prostate epithelial cells

tag: genotype/variation


title: EZH2 K735R_RNAseq_rep1


title: E2 B2 d21 BAL

description: d21 M.tuberculosis BAL sample


title: sequencing of TCG-6-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat2

description:
ArgTCGsgRNA_d0_TCG-6-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

extract_protocol:
PureLink genomic DNA mini kit (Invitrogene; K182000)
genomic DNA was used as template for PCR to amplify specifically the tRNA isodecoder genes of the CRISPR- targeted tRNAs in the population. PCR reaction was conducted using KAPA HiFi HotStart ReadyMixPCR (X2) (kapabiosystems; KK2601), 10µM of each primer and 100ng of genomic DNA in a 60µl total volume reaction, for 25 cycles. Primers and annealing temperatures are listed (Figure2- source data 1). After PCR validation using agarose gel, the PCR product was purified with SPRI-beads using left-side size selection protocol in which the PCR product and beads were mixed at 1:1.5 ratio. Then, each sample was barcoded with a different Illumina barcode while the Forward primer was fixed and the reverse primer included the different barcodes. The barcoding PCR reaction that was conducted using KAPA HiFi HotStart ReadyMixPCR Kit (X2), 10µM of Illumina primers and 0.35-0.7ng of PCR product in a 10µl total volume reaction, for 15 cycles. Additional clean-up step was performed using SPRI beads with left-side size selection protocol in which the PCR product and beads were mixed at 1:1.5 ratio. Samples were pooled in equal amounts and sequenced.

value: Day 0


title: sequencing of TCG-1-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d4_TCG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: EZH2 WT_RNAseq_rep2

value: PtenPC-/-


title: sequencing of TCG-2-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_d4_TCG-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: E2 A4 d21 BAL

description: d21 M.tuberculosis BAL sample


title: E2 A5 d21 BAL

description: d21 M.tuberculosis BAL sample


title: EZH2 WT_RNAseq_rep1


title: E2 A2 d21 BAL

description: d21 M.tuberculosis BAL sample


title: E2 B5 d14 BAL

description: d14 M.tuberculosis BAL sample

value: day 14


title: SETD2 EZH2 KO_RNAseq_rep2

data_processing:
For RNA-Seq, transcriptome reads from Hiseq RNA-Seq experiments were mapped to the reference genome (mm10) by using Bowtie tool. Gene expression levels were quantified by a software package called RSEM. The list of significance was operated by setting fold changes threshold at level of 1.5 and p value < 0.05.
For ChIP-Seq, the 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis.tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp).To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.The two main peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig for ChIP-Seq and count/rpkm for RNA-seq

extract_protocol:
For RNA-seq, total RNA was extracted from the prostatic organoid cells derived from 3-month-old PtenPC+/- and PtenPC+/-; Setd2PC-/- mice with or without Ezh2 deletion, and then subjected to PE150 Hiseq. The chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against H3K27me3 ( Active Motif 39155).
Libraries were prepared according to standard Illumina protocols.


title: mo10.5_rep3

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

hyb_protocol: The Cy3-labeled cDNA were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent's recommended hybridation chamber and oven. Then the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37°C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain raw median signal in green channel.  Quality assessment was first performed on the microarray data.  Spatial images of the foreground and background signals were made for each microarray sample to check any potential image artifacts, using the R/bioconductor package mArray vserion 1.66.0.  The distribution of the data was checked with density and box plots.  The raw microarray signal data were normalized with the quantile normalization method (Bolstad, 2003) to reduce the obscuring variation between microarrays, which might be introduced during the processes of sample preparation, manufacture, fluorescence labeling, hybridization and/or scanning.  Signals were averaged for a small subset of intra-microarray replicate probes.  Between-treatment and between-replicate variations were examined with the pair-wise MvA plots, in which the base 2 log ratios (M) between two samples are plotted against their averaged base 2 log signals (A).  Principal Component analysis (PCA) was also performed to assess sample variability.  The probes of incomplete functional annotation including “unknown”, “predicted gene”, “hypothetical protein” and “RIKEN cDNA” were filtered out in the downstream analysis.

organism: Musculus

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, month 10.5, replicate 3

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

extract_protocol: RNA was prepared using SuperAmp Preparation kit (Miltenyi Biotec, Auburn, CA)following the manufacturer's recommendations. The protocol includes lysis of sorted lymphocytes with Proteinase K, and on-column magnetic isolation of mRNA with small superparamagnetic MACS SuperAmp Microbeads. cDNA was synthesized and amplifiled by a global PCR reaction (Roche). The cDNA was quantified using a NanoDrop-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and quality was mornitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Splenocytes of female DO11.10 mice were transferred into age-matched BALB/c recipients i.v. followed by Vaccinia-OVA virus injection i.p. 24h later. Draining lymph nodes and spleens were extracted at times 0 and 9 days, 5 weeks, 6- and 10.5 months later. Cells were stained and cells positive for CD4, CD44, and KJ1.26 Ab were sorted on a high-performance MoFlo sorter. Cells from sex and age-matched old naïve DO11.10 mice served as naive controls.

value: CD4+ cells

tag: gender

value: Female


title: SETD2 EZH2 KO_RNAseq_rep1


title: mo10.5_rep2

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, month 10.5, replicate 2


title: E2 A3 d21 BAL

description: d21 M.tuberculosis BAL sample


title: mo6_rep3

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, month 6, replicate 3


title: E2 A1 d21 BAL

description: d21 M.tuberculosis BAL sample


title: mo10.5_rep1

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, month 10.5, replicate 1


title: E2 B4 d14 BAL

description: d14 M.tuberculosis BAL sample


title: sequencing of TCG-4-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat2

description:
ArgTCGsgRNA_d0_TCG-4-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

data_processing:
library strategy: amplicon library
Read were trimmed using cutadapt
NHEJ events were quantified using CRISPResso (Pinello et al., 2016)  in the CRISPR-iCas9 targeted samples. The input for the CRISPResso pipeline included both the amplicon sequences of the unedited (WT) tRNA genes and the sgRNA sequences. The minimum identity score for the alignment was set to 0
Genome_build: hg19
Supplementary_files_format_and_content: Read count of WT reads or reads with NHEJ events. Read count of reads with insertions and deletions for the NHEJ reads was calculated as well.

value: iCas9 - ArgTCG sgRNA

value: repeat 2


title: E2 B3 d14 BAL

description: d14 M.tuberculosis BAL sample


title: E2 B2 d14 BAL

description: d14 M.tuberculosis BAL sample


title: sequencing of TCG-6-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat1

description:
ArgTCGsgRNA_d0_TCG-6-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: sequencing of TCG-4-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat1

description:
ArgTCGsgRNA_d0_TCG-4-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: EZH2 KO_RNAseq_rep1


title: sequencing of TCG-5-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat2

description:
ArgTCGsgRNA_d0_TCG-5-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: sequencing of TCG-5-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat1

description:
ArgTCGsgRNA_d0_TCG-5-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: mo6_rep1

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, month 6, replicate 1


title: sequencing of TCG-3-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat2

description:
ArgTCGsgRNA_d0_TCG-3-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: E2 A5 d14 BAL

description: d14 M.tuberculosis BAL sample


title: E2 A4 d14 BAL

description: d14 M.tuberculosis BAL sample


title: wk6_rep3

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, week 6, replicate 3


title: sequencing of TCG-3-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat1

description:
ArgTCGsgRNA_d0_TCG-3-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: SETD2 KO_RNAseq_rep1


title: CTRL_RNAseq_rep2

value: PtenPC+/-


title: sequencing of TCG-2-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat2

description:
ArgTCGsgRNA_d0_TCG-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: mo6_rep2

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, month 6, replicate 2


title: CTRL_RNAseq_rep1


title: sequencing of TCG-2-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat1

description:
ArgTCGsgRNA_d0_TCG-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: sequencing of TCG-1-1 gene in HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat2

description:
ArgTCGsgRNA_d0_TCG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: Skin_WT_T_cells-Exp3-834_IGO

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to mm10 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

source_name: Skin

growth_protocol: 1X10^5 WT CD8+ OT-1 T cells were mixed with 1x10^5 PD-1 -/- CD8+ OT-1 T cells and were co-adoptively transferred to WT recipients one day before infection

extract_protocol: Total RNA was extracted from samples using the RNeasy Mini kit (Life Technologies). Samples were then subject to poly(A) selection using oligo-dT beads (Life Technologies) using Clonetech SMART-Seq v4 Ultra Low Input RNA Kit.

treatment_protocol: Recipient mice were vaccinated by VACV-OVAss on each ear with 1x10^6 and on the base of the tail with 2x10^6 viral p.f.u.  At day 14, WT or PD-1-/- donor CD8+ T cells were isolated from ear skin and sorted into trizol medium. Naïve CD8+ OT-1 T cells were isolated from lymph node and spleen of naive mice by negative selection on MACS beads and stored in trizol medium before RNA extraction.

value: CD8+ T cells

value: Wild type OT-1

value: 1X10^5 WT CD8+ OT-1 T cells were mixed with 1x10^5 PD-1 -/- CD8+ OT-1 T cells and were co-adoptively transferred to WT recipients one day before VACV-OVA skin scarification. At day 14, WT donor CD8+ T cells were isolated from ear skin and sorted into trizol medium.


title: wk6_rep2

source_name: gene expression of CD4 cells of lymph nodes and spleens of female DO11.10 mouse, week 6, replicate 2


title: E2 A2 d14 BAL

description: d14 M.tuberculosis BAL sample


title: SETD2 KO_RNAseq_rep2