title: HeLa-iCas9-LeuTAG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_HeLa_D12_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

tag: cell line

value: HeLa

value: repeat 1

value: tRNA


title: SMARCA4KO_SMARCA2dTAG_dTAG47_72h_H3K27ac

status: Public on Dec 22 2020

type: SRA

city: Vienna

first: Stefan

last: Kubicek

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

library_source: genomic

data_processing:
Read trimming was performed using Skewer (Jiang et al., 2014) for ATAC-seq and ChIP-seq data, Trimmomatic (Bolger et al., 2014) for RNA-seq data or cutadapt for Pro-seq data (Martin, 2011).
ATACseq and ChIP-seq: Read mapping was performed to GRCh38/hg38 using Bowtie2 (Langmead and Salzberg, 2012) and the “-very sensitive” parameter. Only unique reads with a mapping quality > 30 and alignment to the nuclear genome were included in the downstream analyses.
ATAC-seq: Peak calling was performed using MACS2 (Zhang et al., 2008) with the “-nomodel” and “extsize 147” parameters. Peaks overlapping blacklisted features defined in the ENCODE project (Hoffman et al., 2013) were discarded from the analyses.
Pro-seq: Raw reads (FASTQ) were trimmed using cutadapt v1.9.1 -a "TGGAATTCTCGGGTGCCAAGG" --minimum-length=10; trimmed reads were converted to reverse complements using fastx_reverse_complement v0.0.14; Read mapping was performed to a concatenated hg38_dm6_rDNA-U13369 genome using bowtie2 (Langmead and Salzberg, 2012) and filtered by a MAPQ value of 20; number of reads aligning to dm6 were counted with "samtools view | awk '$3 ~ /dm6_/ {++dm6_count}'" and normalization factor alpha=1e6/dm6_count (see PMID: 25437568); only 3' base (Pol II active center) was retained in BED files with "bedtools v2.26.0 bamtobed | awk '($6 == "+") {print $1,$3-1,$3,$4,$5,$6}; ($6 == "-") {print $1,$2,$2+1,$4,$5,$6}'"
RNA-seq: Read mapping was performed using STAR (Dobin et al.,2013) and the Ensembl transcript annotation from version e100 April2020 as reference transcriptome.
Genome_build: hg38
Supplementary_files_format_and_content: txt, raw read counts per region per sample
csv, raw read counts per region per sample
tsv, raw read counts per gene per sample

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HAP1 wildtype (Horizon Discovery C631) and knock-out cells were grown in Iscove's Modified Dulbecco's Medium (IMDM, Thermo Fisher Scientific, 21980-032 or Sigma I3390) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific 10500064) and 1% Pen Strep (100 units/ml Penicillin, 100 µg/ml Streptomycin, Thermo Fisher Scientific, 15140-122) at 37 °C and 5% CO2.

extract_protocol:
ATAC-seq was performed according to Buenrostro et al. with small adaptations (Buenrostro et al., 2015). In brief, 50,000 cells (1:2 drosophila S2 cells : HAP1 cells) were resuspended in 25 µl transposase reaction mix (0.02% digitonin (Promega G9441), 1x TD buffer, 0.08% TDE1 (Nextera DNA Library Preparation Kit, Illumina, FC-121-1031)) and incubated for 30 min, 37°C, 300 rpm. Then DNA was purified using MinElute kit (Qiagen, 28004) and eluted in 11 µl elution buffer. On-plate ATAC-seq was performed as described for ATAC-seq, but without Drosophila spike-ins and performing transposase reaction on the plate. ChIP-seq and RNA-seq was performed as described in Schick et al., 2019. Pro-seq was performed as described in Jaeger et al., 2020.
ATAC-seq: 1 µl was used to determine cycle number for PCR using a qPCR approach. The remaining 10 µl were complemented with 1x NEBnext High-Fidelity PCR master mix (New England BioLabs, M0541), 1.25 µM index primer 1 and 1.25 µM index primer containing a barcode. PCR was performed: 5 min 72°C, 30 sec 98°C, X cycles of 10 sec 98°C + 30 sec 63°C + 1 min 72°C, 1 min 72°C and then cleaned-up using Agencourt AMPure XP beads (Beckman Coulter, A63880). The libraries were checked on a Bioanalyzer instrument using High Sensitivity DNA Chips (Agilent), quantified using Qubit dsDNA HS Assay kit (Thermo Fisher Scientific, Q32854) and pooled. Libraries were sequenced using the Illumina HiSeq3000/4000 platform with the 75 bp paired-end configuration.   ChIP-seq: NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs E7645) was used for the library preparation as described by manufacturer protocol. The quality control of the ChIP samples was confirmed prior to sequencing on Bioanalyzer (Agilent Cat no. 5067-4626). Samples were sequenced on a HiSeq 3000/4000 platform using 50 bp single read configuration.  RNA-seq: RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts. Expression profiling libraries were sequenced on HiSeq 3000/4000 instruments (Illumina, San Diego, CA, USA) in 50-base-pair, single-end mode.  PRO-seq: Finally, RNA was reverse transcribed using RP1 primer with Superscript III and cDNA subjected to a 4x-dilution series test PCR to determine the optimal PCR cycle number for final sequencing library amplification. Full scale amplification with RPI-x indexing primers was then performed in 2x 50 µl reactions per sample for a total of 11-19 cycles. DNA was ethanol precipitated and subjected to 2x 1.1:1 AMPure XP bead left-side size selection according to manufacturer instructions. DNA concentration was determined using the Qubit dsDNA Hs kit and library size distribution was measured with Bioanalyzer. Libraries were pooled to equal molar ratios and sequenced on a HiSeq 3000/4000 system in 50SR mode, yielding ~60 mio reads per sample.

treatment_protocol: Cells were either treated with DMSO, 300 nM dTAG47, 1 µM BRM014, 3 µM ACBI1 or 3 µM cis-ACBI1 for the indicated time.

tag: genotype

value: SMARCA4 KO

tag: dtag

value: SMARCA2 dTAG

tag: treatment

value: 72h dTAG47

tag: bait


title: 17-0001 Bulk

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

country: USA

institute: Indiana University

library_source: transcriptomic

data_processing:
For Illumina Sequencing data, FastQC for sequencing quality check
Adapter sequences were removed with cutadapt (1.14+)
Reads were aligned to the human referece genome Hg38 using STAR with parameters ajusted to short reads and Integrative Genomics Viewer (IGV) alignment.
Expression counts determined by edgeR / rbamtools
The remaining processing and normalization steps described on the paper were not performed on the provided processed data
Genome_build: Hg38
Supplementary_files_format_and_content: csv

molecule: total RNA

source_name: Kidney

extract_protocol:
Kidney tissue was obtained from a clinical biopsy, placed in Michels solution and frozen on OCT within 24 h. 20 um of cross-sectional biopsy tissue was cut on a cryotome and placed in Arcturus Picopure extraction buffer. RNA was extracted according to protocol.
Nephrectomies were obtained and frozen on OCT within 24 h. 20 um of cross-sectional biopsy tissue was cut on a cryotome and placed in Arcturus Picopure extraction buffer. RNA was extracted according to protocol.
SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input
RNA seq, 10 millions input reads per sample

tag: tissue

value: Kidney

tag: disease

value: Reference

tag: tissue source

value: Nephrectomy

tag: segment

value: Bulk

tag: storage

value: OCT at -80C

tag: gender

value: Female


title: miRNA-seq_blood_STZ_10w_1

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

country: Japan

institute: Chuo University

description:
non coding small RNA seq
blood_STZ_10w_1
DIAR STZ 10w serum

data_processing:
Processed by CAP-MIRSeq. See setup files, run_info.txt, sample_info.txt, tool_info.txt
Genome_build: mm10
Supplementary_files_format_and_content: generated Excel file

organism: Mus musculus

source_name: exosome

extract_protocol:
Total RNA was extracted by RNeasy mini kit (Qiagen).
1) Filter Small RNA: Separate RNA segment of different size by PAGE gel,select 18-30nt stripe and recycle. 2) Adaptor  ligation: Prepare connection system, blend and centrifuge, connect warmly for a period of time. 3) RT-PCR: Prepare  reverse transcription system, connect warmly for a period on PCR on PCR instrument, then PCR amplification. 4) Purify  PCR products: Recover the Purified PCR construct by PAGE gel, dissolve the recylced products in EB solution. Finally,  label to finish the library construction. 5) Library quality testing: Use Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-  TimePCR System to test quality and production of the prepared library.

treatment_protocol: Excision of liver tissue, and exosome rich fraction extracted by Exoquick (System Biosciences).

tag: disease state

value: hepatocellular carcinoma

value: serum exosome

tag: time

value: 10 weeks


title: miRNA-seq_blood_STZ_6w_3

description:
non coding small RNA seq
blood_STZ_6w_3
DIAR STZ 6w serum

value: 6 weeks


title: SMARCA4KO_SMARCA2dTAG_24h_dTAG_H3K27ac

value: 24h dTAG47


title: HeLa-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat1

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

country: Israel

institute: Agriculture Research Organization

description:
LeuTAGsgRNA_HeLa_D8_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

data_processing:
library strategy: tRNA-seq
Read were trimmed using homerTool
Alignment was done to the genome and mature tRNA using Bowtie2 (Langmead and Salzberg, 2012) with parameters --very-sensitive-local. Read aligned with equal alignment score to the genome and mature tRNA were annotated as mature tRNA. Reads aligned to multiple tRNA genes were randomly assigned when mapping to identical anticodon, and discarded from the analysis if aligned to different anticodon.
Read count was done using BedTools-coverage count (Quinlan and Hall, 2010).
Variant calling for detection of mutation and indels was done using samtools (Li et al., 2009) command “mpileup” with the parameters: “-A -q1 -d100000”.
Genome_build: hg19
Supplementary_files_format_and_content: read counts of mature tRNA and reads with Indel mutation in the vicinity (5 nt up and downstream) of the sgRNA targeting site, and the maximal read coverage in that location

source_name: HeLa iCas9 - LeuTAG 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). 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:
RNA was extracted using TRI-reagent (Sigma-Aldirch), according to standard protocol.
tRNA sequencing protocol was adapted from Zheng et al., 2015 (Zheng et al., 2015) with minor modification. Small RNA was isolated using SPRI-beads (Agencourt AMPure XP, Beckman Coulter), using dual side size-selection protocol. First RNA and beads were mixed at 1:1.8 ratio, collection the supernatant. The small RNA was isolated by mixing the clear supernatant with bead at 1:0.8 ratio, with addition of X1.34 isopropanol. Small RNA was treated for modification removal using AlkB wt, and D135S, a kind gift from Prof. Tao Pan. Reverse transcription was done using TGIRT™-III Enzyme, with the indicated primers. 3’ adaptor was ligated to the cDNA using T4 ligase (NEB). The cDNA was purified using Dynabeads myOne SILANE (life Technologies) after each step.  The library was amplified using NEBNext PCR mix and cleaned using SPRI-beads. Samples were pooled and sequenced using NextSeq illumina. primers: Reverse-transcription DNA:5’-CACGACGCTCTTCCGATCTT  -3’,  Reverse-transcription RNA:5’-rArGrArUrCrGrGrArArGrArGrCrGrUrCrGrUrG-3’,  3’ adaptor:5’-  CGTCATAGATCGGAAGAGCACA-3’.

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

value: HeLa

tag: crispr construct

value: iCas9- LeuTAGsgRNA

tag: icas9 induction time

value: Day 8

tag: repeat

tag: molecule subtype


title: 17-0001 CD

value: Collecting Duct


title: SMARCA4KO_DMSO_input

value: SMARCA4 KO

value: DMSO


title: miRNA-seq_blood_STZ_6w_1

description:
non coding small RNA seq
blood_STZ_6w_1
DIAR STZ 6w serum


title: miRNA-seq_blood_CTR_12w_3

description:
non coding small RNA seq
blood_CTR_12w_3
DIAR control 12w serum

value: normal control

value: 12 weeks


title: miRNA-seq_blood_CTR_12w_2

description:
non coding small RNA seq
blood_CTR_12w_2
DIAR control 12w serum


title: HeLa-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_HeLa_D4_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

tag: cell line

value: Day 4

value: repeat 1

value: tRNA


title: SMARCA2KO_DMSO_H3K27

tag: genotype

value: SMARCA2 KO


title: HeLa-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_HeLa_D4_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: repeat 2


title: HeLa-iCas9-LeuTAG sgRNA cells, before iCas9 induction, repeat2

description:
LeuTAGsgRNA_HeLa_D0_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: Day 0


title: miRNA-seq_blood_CTR_10w_3

description:
non coding small RNA seq
blood_CTR_10w_3
DIAR control 10w serum

value: serum exosome

value: 10 weeks


title: SMARCA4KO_DMSO_H3K27ac


title: HeLa-iCas9-LeuTAG sgRNA cells, before iCas9 induction, repeat1

description:
LeuTAGsgRNA_HeLa_D0_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv


title: miRNA-seq_blood_CTR_12w_1

description:
non coding small RNA seq
blood_CTR_12w_1
DIAR control 12w serum


title: HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_HeLa_D12_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

source_name: HeLa iCas9 - ArgTCG sgRNA

value: iCas9- ArgTCGsgRNA

value: Day 12


title: SMARCA2KO_DMSO_input


title: R2_6h_control

description:
on-plate ATAC-seq
count_matrix_raw_atac_BRM014_ACBI1.csv

value: wild-type

value: 6h cis-ACBI1


title: R2_6h_BI_protac

value: 6h ACBI1


title: HeLa-iCas9-ArgTCG sgRNA cells, day 12 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_HeLa_D12_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: HeLa


title: miRNA-seq_blood_CTR_10w_2

description:
non coding small RNA seq
blood_CTR_10w_2
DIAR control 10w serum


title: R2_5min_N

value: 5min BRM014


title: miRNA-seq_blood_CTR_10w_1

description:
non coding small RNA seq
blood_CTR_10w_1
DIAR control 10w serum

value: normal control


title: HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_HeLa_D8_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: Day 8


title: miRNA-seq_blood_CTR_6w_3

description:
non coding small RNA seq
blood_CTR_6w_3
DIAR control 6w serum

value: 6 weeks


title: HeLa-iCas9-ArgTCG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_dHeLa_D8_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

value: repeat 1


title: R2_5min_DMSO

value: 5min DMSO


title: miRNA-seq_blood_CTR_6w_2

description:
non coding small RNA seq
blood_CTR_6w_2
DIAR control 6w serum


title: SMARCA4KO_SMARCA2dTAG_3h_dTAG_H3K27ac

value: SMARCA4 KO

tag: dtag

value: SMARCA2 dTAG

value: 3h dTAG47


title: HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
ArgTCGsgRNA_HeLa_D4_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: Day 4

value: repeat 2

value: tRNA


title: R2_30min_N

tag: treatment

value: 30min BRM014


title: HeLa-iCas9-ArgTCG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
ArgTCGsgRNA_HeLa_D4_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

value: iCas9- ArgTCGsgRNA


title: BEMP-2

city: Parkville

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

data_processing:
Sequence reads were alligned using the Subread aligned
Genewise counts were obtained using FeatureCounts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Haemopedia-Mouse-RNASeq_raw.txt is the raw counts as given by featureCounts
Supplementary_files_format_and_content: Haemopedia-Mouse-RNASeq_rpkm.txt gives gene wise RPKM
Supplementary_files_format_and_content: Haemopedia-Mouse-RNASeq_rpkm.txt

source_name: Bipotential Erythroid Megakaryocyte Progenitors (BEMP)

growth_protocol: All cells were purified from mice between 7 and 12 weeks of age.

extract_protocol:
RNA was isolated from two biological repliates (RNAeasy plus micro kit, QIagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

tag: cell type short

value: BEMP

tag: strain

tag: antibodies

value: Lin:- cKit:+ Sca1:- CD150:+ FcgRII/III (CD16/32):- Endoglin:lo CD9:lo

value: Bone Marrow

tag: growth

value: Bone marrow was harvested from femurs and tibias, flushed with a needle and processed to a single cell suspension. Red cell removal buffer was applied

tag: lineage

value: Restricted Potential Progenitor

tag: invitrotreatment


title: SkBr-3

city: Guangzhou

first: YY

last: Xiong

address: Xingangxi Rd

department: School of Life Sciences

country: China

institute: Sun Yat-sen University

data_processing:
the raw reads files were provided as input for Arriba (v1.0.0) to call fusion events, by integrating annotations from GENCODE v28, MiTranscriptome v2, LNCiPedia v5.2, and NONCODE v5.
Genome_build: hg38
Supplementary_files_format_and_content: fusion calls from RNA-seq for SkBr-3 cells; each line represents a fusion event with two breakpoints in two genes, respectively, with other related information

molecule: polyA RNA

source_name: breast cancer cells

extract_protocol:
Total RNA of these two cells were extracted using TRIzol according to the manufacturer’s instructions (Invitrogen, Thermo Scientific, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: breast cancer cells


title: R2_24h_N

value: wild-type


title: HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat2

description:
ArgTCGsgRNA_HeLa_D0_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

value: HeLa

value: Day 0


title: BEMP-1

value: Bipotential Erythroid Megakaryocyte Progenitors (BEMP)

tag: tissue


title: 293T_dCas9-VP64_sgL1ASP_3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: 293T cells expressing dCas9-VP64 together with sgL1ASP #3

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software was used for base calling.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: 293T cells expressing dCas9-VP64 with sgL1ASP #3

extract_protocol:
Total RNA was purified using the miRNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.


title: 293T_dCas9-VP64_sgL1ASP_1

description: 293T cells expressing dCas9-VP64 together with sgL1ASP #1

source_name: 293T cells expressing dCas9-VP64 with sgL1ASP #1


title: HeLa-iCas9-ArgTCG sgRNA cells, before iCas9 induction, repeat1

description:
ArgTCGsgRNA_HeLa_D0_rep1
processed data file: maturetRNA_tRNAtargetedHeLa_rep1.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep1.csv

value: repeat 1


title: R2_24h_BI_protac

value: 24h ACBI1


title: CD9Hi-2

source_name: CD9Hi bipotential megakaryocyte erythroid progenitors

value: Lin:- cKit:+ Sca1:- CD150:+ FcgRII/III (CD16/32):- Endoglin:lo CD9:hi


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, un-treated cells, un-sorted cells, repeat2

description:
WI38fast_arrest_UntreatedUnsorted_rep2
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

data_processing:
library strategy: amplicon library
Growth competition:  SeqPrep (https://github.com/jstjohn/SeqPrep) was used to merge paired reads into a single contig, to increase sequence fidelity over regions of dual coverage. The size of each contig was then compared to the amplicon’s length. Next, the forward and reverse primers were found on each contig (allowing for 2 mismatches) and trimmed out. This step was performed for both the forward and reverse complement sequences of the contig, to account for non-directional ligation of the adaptors during library preparation. After the primers were trimmed, the contig was tested again for its length to ensure no Indels had occurred. Contigs were then compared sequentially to all sgRNAs, comparing the sequence of each contig to the sequence of each sgRNA. Any contig without a matching sgRNA within two mismatches or less was discarded. Contigs with more than a single matching sgRNA with the same reliability were also discarded due to ambiguity.
Cell cycle arrest signals:  Reads were trimmed using Cutadapt and then clustered into unique sequences using vsearch (Rognes et al., 2016). Each unique read was then aligned to the matched sgRNA sequence, allowing up to two mismatches
Genome_build: sgRNA name sgRNA sequence  ArgACG-sgRNA GATTCCAGGTTCGACTCC  ProAGG-sgRNA GGGTATGATTCTCGCTTA  LeuCAG-sgRNA GTCTAAGGCGCTGCGTTC  TrpCCA-sgRNA GCGTGTTCAAATCACGTC  GlyCCC-sgRNA GAACCCGGGTCGCAAGAA  ArgCCG-sgRNA GGATAAGGCGTCTGATTC  SerCGA-sgRNA GTTGGACTCGAAATCCAA  ProCGG-sgRNA GGGTATGATTCTCGCTTC  ThrCGT-sgRNA GACCGACGCCTTACCACT  GlyGCC-sgRNA GGGCCGGGAATCGAACCC  IleAAT-sgRNA GTGGTGCTAATAACGCCA  AsnATT-sgRNA GCAATCGGTCAGAGCGTT  LeuCAA-sgRNA GGATGGCCGAGTGGTCTA  ValTAC-sgRNA GTCTGCTTTACACGCAGA  LeuTAG-sgRNA GTCTAAGGCGCTGGATTT  IleTAT-sgRNA GTGAGTTCGAGCCTCACC  ArgTCG-sgRNA GGATAAGGCGTCTGACTT  ArgTCT-sgRNA GCGCAATGGATAGCGCAT  GluTTC-sgRNA GATTCCTGGTTTTCACCC  LysTTT-sgRNA GGGTTCAAGTCCCTGTTC
Supplementary_files_format_and_content: read count of each sgRNA in each sample

source_name: WI38fast-iCas9- p21p-mCherry- pooled sgRNA

growth_protocol: Growth comeptition  HeLa- iCas9 with pooled sgRNAs  cells 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 and slow iCas9 with pooled sgRNAs cells 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), 2µg/ml Puromycin (for sgRNA selection, InvivoGen; BLL-38-02A. notice that WI38 dervied cells are already resistant to Puromycine, for more information see "Materials and Methods") and 1µg/ml Doxycycline (for iCas9 induction, Sigma-Aldrich; 10592-13-9).   Upon iCas9 induction, each cell population was samples every 3-4 days, and fresh medium containing all antibiotics was replaced every two days for 12 days.  Cell cycle arrest signals  WI38 fast iCas9- p21p-mCherry- pooled sgRNA cells were grown is previously described. The medium was supplemented with 200µg/ml Hygromycin (for iCas9 selection, Thermo Fisher; 10687010), 10 µg/ml Blasticidin  and 1µg/ml Doxycycline (for iCas9 induction, Sigma-Aldrich; 10592-13-9).

extract_protocol:
PureLink genomic DNA mini kit (Invitrogene; K182000)
Growth competition:  PCR reaction was conducted using iProof master mix (X2), 10µM of each primer and 20ng of genomic DNA in a 50µl total volume reaction, for 26 cycles, Tm = 64°C. The primers used to amplify the sgRNA region were:  Forward primer- GCTTACCGTAACTTGAAAGTATTTCGATTTCTTGG  Reverse primer- CTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAAC   After PCR clean-up using Wizard SV Gel and PCR Clean-Up (Promega; A9281), samples were run in 2% agarose gel to ensure that the PCR product is compose of a single amplicon in the appropriate size. Next, Illumina HiSeq 2000 libraries were prepared using the sequencing library module from (Blecher-Gonen et al., 2013). Briefly, blunt ends were repaired, Adenine bases were added to the 3' end of the fragments, barcode adapters containing a T overhang were ligated, and finally the adapted fragments were amplified. The process was repeated for each sample with a different Illumina DNA barcode for multiplexing, and then all samples were pooled in equal amounts and sequenced.   Cell cycle arrest signals:  PCR reaction was conducted using 2X KAPA HiFi HotStart ReadyMix, 10µM of each primer and 20ng of genomic DNA extracted from the samples in a 50µl total volume reaction, for 20 cycles, Tm = 58°C. We used shifted primers to increase library complexity. PCR products were 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: Cell cycle arrest signals:  following 3 days of iCas9 induction, ancestor cell population was split to three populations, in which each population was treated differently. To activate senescence, cells were grown with media containing 2.5uM Etoposide (Sigma-Aldrich; 33419-42-0). To active quiesence, cells were grown with serum- free media. The third population continued to grow without any treatment.   All samples:  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: day of sampling

value: after 3 days of iCas9 induction and 2 days with normal medium

value: repeat 2


title: 293T_dCas9-VP64_mock

description: 293T cells expressing dCas9-VP64 together with mock

source_name: 293T cells expressing dCas9-VP64 with mock


title: R2_1h_N

value: 1h BRM014


title: R2_24h_DMSO

value: 24h DMSO


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, un-treated cells, un-sorted cells, repeat1

description:
WI38fast_arrest_UntreatedUnsorted_rep1
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv


title: CD9Hi-1

value: CD9Hi bipotential megakaryocyte erythroid progenitors


title: FcgRCD150-2

source_name: FcgammaR+ CD150+ Progenitor

value: FcgammaR+ CD150+ Progenitor

value: Lin:- cKit:+ Sca1:- CD150:+ FcgRII/III (CD16/32):+ CD9:hi


title: R2_6h_N

description:
on-plate ATAC-seq
count_matrix_raw_atac_BRM014_ACBI1.csv

value: 6h BRM014


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, un-treated cells, low mCherry sorted cells, repeat2

description:
WI38fast_arrest_UntreatedLowmCh_rep2
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv


title: FcgRCD150-1

value: Bone Marrow

value: Bone marrow was harvested from femurs and tibias, flushed with a needle and processed to a single cell suspension. Red cell removal buffer was applied

value: Restricted Potential Progenitor


title: miRNA-seq_blood_CTR_6w_1

description:
non coding small RNA seq
blood_CTR_6w_1
DIAR control 6w serum

tag: disease state

value: normal control

value: serum exosome

tag: time

value: 6 weeks


title: Bcells_Input

city: Sendai

first: Kyoko

last: Ochiai

address: 2-1, Seiryo-machi, Aobaku

department: Biochemistry

institute: Tohoku University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.
Tag sequences were aligned to the mm10 genome assembly using bowtie2-2.3.2.
Peaks were identified using the FindPeaks tool in the HOMER package with input DNA tags as background distribution.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files reporting ChIP-seq peaks with input DNA tags as background distribution

source_name: Activated B cells, 1 and 3 days

extract_protocol:
Activated B cells were fixed 1% formaldehyde, followed by quenching with 125mM of glycine. The cells were washed with ice-cold PBS and were lysed. The crosslinked chromatin was shared with a Bioruptor Sonicator (CosmoBio) and target protein-DNA complexes were isolated with antibody.
Purified ChIP DNA was carried for preparing DNA libraries, and clonally amplified on a flow cell and sequenced on HiSeq2500 (HiSeq Control Software v2.2.38, Illumina) with 51-mer paired-end sequence. Image analysis and base calling were performed using Real-Time Analysis Software (v1.18.61, Illumina).

treatment_protocol: Splenic B cells were cultured in RPMI-1640 medium supplemented with 100 U/mL IL-2, 5 ng/mL IL-4, 1.5 ng/mL IL-5, 0.2 ng/mL CD40 ligand, 0.01 ng/mL NP-ficoll, 10% FBS 10mM HEPES, 1 mM Na-Pyruvate, 0.1 mM non-essential amino acids and penicilli/streptmycin. For PC4 transduction, retrovirus preparation and transduction with MSCV FLAG-PC4 were performed as descrived previously (Ochiai et al. Nature Immunology 13,300-307, 2012).

tag: genotype/variation

value: splenic B cells

tag: chip antibody

tag: vendor (antibody)

tag: catalog#  (antibody)


title: R2_10min_N

tag: genotype

value: wild-type

value: 10min BRM014


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, un-treated cells, low mCherry sorted cells, repeat1

description:
WI38fast_arrest_UntreatedLowmCh_rep1
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

tag: cell line

value: after 3 days of iCas9 induction and 2 days with normal medium

tag: repeat

value: repeat 1


title: Bcells_H3K27ac_ChIPseq

source_name: Activated B cells, 3 days

tag: cell type

value: Abcam


title: R2_24h_control

tag: treatment

value: 24h cis-ACBI1


title: R1_6h_control

value: 6h cis-ACBI1


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, un-treated cells, high mCherry sorted cells, repeat2

description:
WI38fast_arrest_UntreatedHighmCh_rep2
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

value: repeat 2


title: GMP_IRF8hi-2

source_name: IRF8 High Granulocyte Macrophage Progenitor

tag: cell type short

tag: strain

value: C57BL/6 IRF8-GFP

tag: antibodies


title: Bcells_IRF4_ChIPseq_rep2

value: Santa Cruz


title: GMP_IRF8hi-1

value: IRF8 High Granulocyte Macrophage Progenitor

value: Bone Marrow

tag: growth

tag: lineage

tag: invitrotreatment


title: R1_6h_N

value: 6h BRM014


title: Bcells_IRF4_ChIPseq_rep1


title: R1_6h_BI_protac

value: 6h ACBI1


title: R1_5min_N

value: 5min BRM014


title: GMP_IRF8int-2

tag: tissue

value: Bone marrow was harvested from femurs and tibias, flushed with a needle and processed to a single cell suspension. Red cell removal buffer was applied

value: Restricted Potential Progenitor


title: R1_5min_DMSO

value: wild-type

value: 5min DMSO


title: GMP_IRF8int-1


title: GMP_IRF8lo-2

source_name: IRF8 Low Granulocyte Macrophage Progenitor


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Serum starvation- treated cells, un-sorted cells, repeat1

description:
WI38fast_arrest_SerStarvUnsorted_rep1
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

tag: day of sampling

value: after 3 days of iCas9 induction and 2 days with Serum- free medium


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Serum starvation- treated cells, low mCherry sorted cells, repeat2

description:
WI38fast_arrest_SerStarvLowmCh_rep2
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv


title: GMP_IRF8lo-1

value: IRF8 Low Granulocyte Macrophage Progenitor


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Serum starvation- treated cells, low mCherry sorted cells, repeat1

description:
WI38fast_arrest_SerStarvLowmCh_rep1
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

value: repeat 1


title: PreGMFlt3Pos-2

source_name: Flt3+ Pre Granulocyte Macrophage Progenitor

value: Lin:- cKit:+ Sca1:- CD150:- FcgRII/III (CD16/32):- Endoglin:- Flt3:+


title: R1_24h_control

value: 24h cis-ACBI1


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Serum starvation- treated cells, high mCherry sorted cells, repeat2

description:
WI38fast_arrest_SerStarvHighmCh_rep2
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

value: repeat 2


title: R1_24h_N


title: NaIO3-CaPB 3

city: Shanghai

first: Gu

last: Ping

address: Manufacturing Road, 833

department: Department of Ophthalmology

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Solexa pipeline v1.8 software used for basecalling.
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The differentially expressed genes and transcripts were filtered using R package Ballgown
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: Retinal pigment epithelial (RPE) cells

growth_protocol: Human ARPE-19 cells were cultured in DMEM/F12 medium supplemented with penicillin/streptomycin and 10% FBS at 37 °C with 5% CO2 in incubator.

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: ARPE-19 cells were pretreated with CaPB for 1 hour, followed by treatment with NaIO3  for 24 h

value: ARPE-19 cells

tag: passages

value: NaIO3-induced human ARPE-19 cells with CaPB treatment

value: Retina


title: PreGMFlt3Pos-1

value: Flt3+ Pre Granulocyte Macrophage Progenitor

value: Bone Marrow


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Serum starvation- treated cells, high mCherry sorted cells, repeat1

description:
WI38fast_arrest_SerStarvHighmCh_rep1
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv


title: NaIO3-CaPB 2


title: PreGMFlt3Neg-2

source_name: Flt3- Pre Granulocyte Macrophage Progenitor

value: Lin:- cKit:+ Sca1:- CD150:- FcgRII/III (CD16/32):- Endoglin:- Flt3:-


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, un-treated cells, high mCherry sorted cells, repeat1

description:
WI38fast_arrest_UntreatedHighmCh_rep1
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

value: after 3 days of iCas9 induction and 2 days with normal medium


title: R1_24h_DMSO

value: 24h DMSO


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Etoposide- treated cells, 1 week after Etoposide treatment, repeat2

description:
WI38fast_arrest_1weekEto_rep2
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

value: after 3 days of iCas9 induction 2 days with 2.5uM Etoposide and then 1 week with no Etoposide


title: R1_24h_BI_protac

value: wild-type

value: 24h ACBI1


title: PreGMFlt3Neg-1

value: Flt3- Pre Granulocyte Macrophage Progenitor

value: Bone marrow was harvested from femurs and tibias, flushed with a needle and processed to a single cell suspension. Red cell removal buffer was applied

value: Restricted Potential Progenitor


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Etoposide- treated cells,1 week after Etoposide treatment, repeat1

description:
WI38fast_arrest_1weekEto_rep1
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

value: repeat 1


title: NaIO3-CaPB 1


title: R1_30min_N

value: 30min BRM014


title: NaIO3 3

value: NaIO3-induced human ARPE-19 cells


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Etoposide- treated cells, un-sorted cells, repeat2

description:
WI38fast_arrest_EtoUnsorted_rep2
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

value: after 3 days of iCas9 induction and 2 days with 2.5uM Etoposide

value: repeat 2


title: R1_1h_N

value: 1h BRM014


title: NaIO3 2

value: ARPE-19 cells

value: Retina


title: R1_10min_N

value: 10min BRM014


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Serum starvation- treated cells, un-sorted cells, repeat2

description:
WI38fast_arrest_SerStarvUnsorted_rep2
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

value: after 3 days of iCas9 induction and 2 days with Serum- free medium


title: HAP1 SMARCC2 KO DMSO_2

data_processing:
Read trimming was performed using Skewer (Jiang et al., 2014)
Read mapping was performed to GRCh38/hg38 using Bowtie2 (Langmead and Salzberg, 2012) and the “-very sensitive” parameter. Only unique reads with a mapping quality > 30 and alignment to the nuclear genome were included in the downstream analyses.
Peak calling was performed using MACS2 (Zhang et al., 2008) with the “-nomodel” and “extsize 147” parameters. Peaks overlapping blacklisted features defined in the ENCODE project (Hoffman et al., 2013) were discarded from the analyses.
Genome_build: hg38
Supplementary_files_format_and_content: txt, raw read counts per region per sample

extract_protocol:
ATAC-seq was performed according to Buenrostro et al. with small adaptations(Buenrostro et al., 2015). In brief, 50,000 cells (1:2 drosophila S2 cells : HAP1 cells) were resuspended in 25 µl transposase reaction mix (0.02% digitonin (Promega G9441), 1x TD buffer, 0.08% TDE1 (Nextera DNA Library Preparation Kit, Illumina, FC-121-1031)) and incubated for 30 min, 37°C, 300 rpm. Then DNA was purified using MinElute kit (Qiagen, 28004) and eluted in 11 µl elution buffer.
1 µl was used to determine cycle number for PCR using a qPCR approach. The remaining 10 µl were complemented with 1x NEBnext High-Fidelity PCR master mix (New England BioLabs, M0541), 1.25 µM index primer 1 and 1.25 µM index primer containing a barcode. PCR was performed: 5 min 72°C, 30 sec 98°C, X cycles of 10 sec 98°C + 30 sec 63°C + 1 min 72°C, 1 min 72°C and then cleaned-up using Agencourt AMPure XP beads (Beckman Coulter, A63880). The libraries were checked on a Bioanalyzer instrument using High Sensitivity DNA Chips (Agilent), quantified using Qubit dsDNA HS Assay kit (Thermo Fisher Scientific, Q32854) and pooled. Libraries were sequenced using the Illumina HiSeq3000/4000 platform with the 75 bp paired-end configuration.
ATAC-seq was performed according to Buenrostro et al. with small adaptations(Buenrostro et al., 2015). In brief, 50,000 cells (1:2 drosophila S2 cells : HAP1 cells) were resuspended in 25 µl transposase reaction mix (0.02% digitonin (Promega G9441), 1x TD

treatment_protocol: Cells were either treated with DMSO or 300 nM dTAG47 for the indicated time.

tag: genotype/variation

value: SMARCC2 KO


title: 2i R1 SET KO1 ESCs 4d RA

city: Jerusalem

first: Eran

last: Meshorer

address: Institute of Life Sciences, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram

department: Department of Genetics

institute: The Hebrew University of Jerusalem

description: 4d RA differentiation protocol

data_processing:
Sequenced reads were aligned with STAR (v2.5.4b) using default parameters to the mouse genome and transcriptome from ENSEMBL (GRCm38.97)
Gene counts were obtained using featureCounts (Subread package v2.0.0) with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each gene and its genomic coordinates for every sample

source_name: Embryonic stem cells

growth_protocol: R1 and KH2 mESCs were cultured on MEF coated plates, in DMEM (Sigma) supplemented with 15% FBS (Biological Industries), L‐glutamine, 1X MEM non‐essential amino acids, Sodium Pyruvate, 1x Penstrep, 0.2 mM β-ME and LIF.

extract_protocol:
Total RNA extraction was performed using RNeasy Mini Kit (Qiagen).
500ng of RNA was used to generate libraries with QuantSeq 3’ mRNASeq Kit (Lexogen) according to manufacturer's protocol.

value: Embryonic stem cells

value: SET-/-

value: 4d Retanoic Acid


title: NaIO3 1


title: Y1705161

city: Wenzhou

first: Xin

last: Liao

address: Wenzhou Medical University, University Town, Chashan, Wenzhou, Zhejiang, P.R China

department: Institute of Genomic Medicine

institute: Wenzhou Medical University

data_processing:
Illumina bcl2fastq software used for basecalling
raw reads were trimmed using Cutadapt adapters and low-quality reads were filtered using Trim Galore. Quality-control reports of sequence reads was obtained through FastQC software.Then, the sequencing data was aligned to the human reference genome hg38 using STAR software.
The read counts files were filtered with low expression and normalized by the DEseq2 package
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: salivary glands

extract_protocol:
Total RNA from frozen salivary glands samples were isolated using TRIzol® Reagent(Invitrogen) and RNA purity was checked using the Nano Photometer® spectrophotometer (IMPLEN, CA, USA).
The high-quality of RNA (RNA integrity numbers (RIN) >9) for cDNA library preparations was assessed by Bioanalyzer 2100 system using the Agilent RNA 6000 Nano kit (Agilent Technologies, CA, USA). Sequencing libraries were constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) with the input material of 3μg of RNA per sample.

value: salivary glands

tag: diagnosis

value: pSS


title: NaiveB_RRBS_rep1

data_processing:
Reads were aligned to mouse genome (mm9).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files reporting the distribution of DNA methylation.

source_name: Naive B cells

extract_protocol:
Genomic DNA was isolated from B1-8hi splenic B cells using chloroform extraction and ethanol precipitation.
RRBS libraries were generated using 20 ng genomic DNA, subjected to MspI digestion (NEB), end repair/dA-tailing reaction using Klenow 3’-5’ exo- (NEB) and ligation by Illumina sequencing adapters using T4 DNA ligase (NEB). The 150-350 bp fragments was extracted from gel, and treated with sodium bisulphite using EZ DNA Methylation-Gold Kit (Zymo Research). Followed by the library amplification and indexing using KAPA HiFi Hot-Start Uracil+ ReadyMix (Kapa Biosystems), purified libraries were sequenced on HiSeq 2500 platform (Illumina). The methylation status of each cytosine was calculated using the Bismark methylation.

value: Splenic B cells

value: Naive


title: NaiveB_RRBS_rep2


title: 2h R1 SET KO1 ESCs 4d RA

description: 4d RA differentiation protocol


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Etoposide- treated cells, low mCherry sorted cells, repeat2

description:
WI38fast_arrest_EtoLowmCh_rep2
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Etoposide- treated cells, low mCherry sorted cells, repeat1

description:
WI38fast_arrest_EtoLowmCh_rep1
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

value: repeat 1


title: HAP1 SMARCC1 KO DMSO_2

value: SMARCC1 KO


title: Y1704281


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Etoposide- treated cells, high mCherry sorted cells, repeat2

description:
WI38fast_arrest_EtoHighmCh_rep2
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

value: after 3 days of iCas9 induction and 2 days with 2.5uM Etoposide


title: 2g R1 SET WT ESCs 4d RA

description: 4d RA differentiation protocol

value: Wt


title: HAP1 ARID2 KO DMSO_2

value: ARID2 KO


title: Y1704182


title: HAP1 SMARCA2 KO DMSO_2

value: SMARCA2 KO


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Etoposide- treated cells, high mCherry sorted cells, repeat1

description:
WI38fast_arrest_EtoHighmCh_rep1
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv


title: Y1704141


title: 2f R1 SET KO2 ESCs rep 3


title: HAP1 SMARCA4 KO DMSO_2

value: SMARCA4 KO


title: 2e R1 SET KO2 ESCs rep 2


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, after 3 days of iCas9 induction, repeat2

description:
WI38fast_arrest_ancestor_rep2
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

value: day 3 of iCas9 induction

value: repeat 2


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, Etoposide- treated cells,un-sorted cells, repeat1

description:
WI38fast_arrest_EtoUnsorted_rep1
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv


title: HAP1 WT DMSO_2

value: wild-type


title: 2e R1 SET KO2 ESCs rep 1

value: Embryonic stem cells


title: 2d R1 SET KO1 ESCs rep 3

value: SET-/-


title: HAP1 SMARCA4KO_SMARCA2dTAG_C8 dTAG 47 2h_2

tag: dtag

value: SMARCA2 dTAG

value: 2h 300 nM dTAG47

tag: time point


title: WI38fast-iCas9- p21p-mCherry pooled sgRNA cells, after 3 days of iCas9 induction, repeat1

description:
WI38fast_arrest_ancestor_rep1
processed data file: sgRNAseq_CellCycleArrestSignals_allSamples.csv

tag: cell line


title: Y1702101

value: salivary glands

value: pSS


title: HAP1 SMARCA4KO_SMARCA2dTAG_C8 dTAG 47 6h_2

value: 6h 300 nM dTAG47


title: sequencing of CGA-4-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat1

description:
SerCGAsgRNA_d8_CGA-4-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.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.

source_name: WI38 fast 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.

value: WI38 fast

tag: crispr construct

value: iCas9 - SerCGA sgRNA

tag: icas9 induction

value: Day 8

tag: the sequenced trna gene

tag: repeat


title: 2c R1 SET KO1 ESCs rep 1

tag: cell type

tag: genotype


title: Y1612231


title: HAP1 SMARCA4KO_SMARCA2dTAG_C8 dTAG 47 24h_2

tag: treatment

value: 24h 300 nM dTAG47


title: HAP1 SMARCA4KO_SMARCA2dTAG_C8 dTAG 47 3h_2

value: 3h 300 nM dTAG47


title: HAP1 SMARCA4KO_SMARCA2dTAG_C8 dTAG 47 72h_2

value: 72h 300 nM dTAG47


title: sequencing of CGA-3-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat3

description:
SerCGAsgRNA_d8_CGA-3-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: repeat 3


title: Y1704061


title: 2b R1 SET WT ESCs rep 3

value: Wt


title: sequencing of CGA-3-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat2

description:
SerCGAsgRNA_d8_CGA-3-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: repeat 2


title: 2d R1 SET KO1 ESCs rep 2


title: Y1612091


title: Y1612021


title: HAP1 SMARCA4KO_SMARCA2dTAG_C8 DMSO_2

value: SMARCA4 KO

value: DMSO


title: Y1611101


title: Y1702211


title: HAP1 SMARCC1KO_SMARCC2dTAG_F1 dTAG 47 2h_2

value: SMARCC1 KO

value: SMARCC2 dTAG


title: 2a R1 SET WT ESCs rep 2

value: Embryonic stem cells


title: 2a R1 SET WT ESCs rep 1


title: sequencing of CGA-3-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat1

description:
SerCGAsgRNA_d8_CGA-3-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: sequencing of CGA-2-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat3

description:
SerCGAsgRNA_d8_CGA-2-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: sequencing of CGA-4-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat3

description:
SerCGAsgRNA_d8_CGA-4-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: Y1610271

value: salivary glands


title: sequencing of CGA-4-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat2

description:
SerCGAsgRNA_d8_CGA-4-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: sequencing of CGA-2-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat2

description:
SerCGAsgRNA_d8_CGA-2-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: HAP1 SMARCC1KO_SMARCC2dTAG_F1 dTAG 47 3h_2


title: Y1610201

value: pSS


title: 2b R1 SET WT ESCs rep 4


title: HAP1 SMARCC1KO_SMARCC2dTAG_F1 dTAG 47 6h_2

value: 6h 300 nM dTAG47


title: KH2 SETa ESCs (+dox) rep 2

description: KH2 cell line with inserted SETa-HA construct under the control of a tetR doxycycline (Dox)-inducible promoter

value: SETa-HA

value: DOX (1 μg/mL) for 24h


title: Y1610111


title: KH2 SETa ESCs (+dox) rep 1


title: sequencing of CGA-2-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat1

description:
SerCGAsgRNA_d8_CGA-2-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: WI38 fast

value: iCas9 - SerCGA sgRNA

value: Day 8


title: HAP1 SMARCC1KO_SMARCC2dTAG_F1 dTAG 47 24h_2

value: 24h 300 nM dTAG47


title: sequencing of CGA-1-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat3

description:
SerCGAsgRNA_d8_CGA-1-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: repeat 3


title: Y1609211


title: KH2 SETa ESCs rep 1


title: N1703281

value: non-pSS


title: sequencing of CGA-1-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat2

description:
SerCGAsgRNA_d8_CGA-1-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: repeat 2


title: miRNA-seq_blood_STZ_6w_2

description:
non coding small RNA seq
blood_STZ_6w_2
DIAR STZ 6w serum

source_name: exosome

tag: disease state

value: hepatocellular carcinoma

value: serum exosome

tag: time

value: 6 weeks


title: HAP1 WT SMARCA4dTAG_F1 dTAG 47 3h_2

value: wild-type

value: SMARCA4 dTAG

value: 3h 300 nM dTAG47


title: HAP1 WT SMARCA4dTAG_F1 dTAG 47 2h_2

value: 2h 300 nM dTAG47


title: sequencing of CGA-1-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 8 of iCas9 induction, repeat1

description:
SerCGAsgRNA_d8_CGA-1-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: SMARCA4KO_SMARCA2dTAG_24h_dTAG_input

value: SMARCA4 KO

value: SMARCA2 dTAG

value: 24h dTAG47

tag: bait


title: KH2 SETa ESCs rep 2

value: Embryonic stem cells

value: SETa-HA


title: 1e R1 SET KO2 ESCs rep 1

value: SET-/-


title: HAP1 SMARCC1KO_SMARCC2dTAG_F1 dTAG 47 72h_2

value: SMARCC1 KO

value: SMARCC2 dTAG

value: 72h 300 nM dTAG47


title: sequencing of CGA-4-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat2

description:
SerCGAsgRNA_d4_CGA-4-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: WI38 fast

value: iCas9 - SerCGA sgRNA

value: Day 4

value: repeat 2


title: N1701241

tag: tissue

value: salivary glands

value: non-pSS


title: 1c R1 SET KO1 ESCs rep 1


title: sequencing of CGA-4-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat1

description:
SerCGAsgRNA_d4_CGA-4-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: N1709057


title: sequencing of CGA-4-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat3

description:
SerCGAsgRNA_d4_CGA-4-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: repeat 3


title: N1701243


title: HAP1 WT SMARCA4dTAG_F1 dTAG 47 6h_2

value: wild-type

value: SMARCA4 dTAG

value: 6h 300 nM dTAG47


title: N1701161


title: 1f R1 SET KO2 ESCs rep 2


title: HeLa-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_HeLa_D8_rep2
processed data file: maturetRNA_tRNAtargetedHeLa_rep2.csv
processed data file: maturetRNA_Indel_tRNAtargetedHeLa_rep2.csv

source_name: HeLa iCas9 - LeuTAG sgRNA

value: HeLa

value: iCas9- LeuTAGsgRNA

tag: icas9 induction time

value: Day 8

tag: molecule subtype

value: tRNA


title: sequencing of CGA-3-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat3

description:
SerCGAsgRNA_d4_CGA-3-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: HAP1 WT SMARCA4dTAG_F1 dTAG 47 24h_2

tag: genotype/variation

value: 24h 300 nM dTAG47


title: 1b R1 SET WT ESCs rep 2

value: Embryonic stem cells

value: Wt


title: HAP1 WT SMARCA4dTAG_F1 dTAG 47 72h_2

tag: dtag

value: 72h 300 nM dTAG47


title: 1d R1 SET KO1 ESCs rep 2

value: SET-/-


title: N1701063

tag: diagnosis


title: sequencing of CGA-3-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat2

description:
SerCGAsgRNA_d4_CGA-3-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

tag: cell line

value: WI38 fast

value: iCas9 - SerCGA sgRNA

value: Day 4


title: N1612131

value: salivary glands

value: non-pSS


title: HAP1 WT SMARCA4dTAG_F1 DMSO_2

value: wild-type

value: DMSO


title: sequencing of CGA-3-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat1

description:
SerCGAsgRNA_d4_CGA-3-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

tag: crispr construct


title: HAP1 ARID2KO_SMARCA4dTAG_F5 dTAG 47 2h_2

value: ARID2 KO

value: SMARCA4 dTAG

value: 2h 300 nM dTAG47

tag: time point


title: DIAR STZ 12w liver 38

data_processing:
cutadapt -b AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT filename.fq.gz > filename_cutadapt.fq.gz
hisat2  -q -x ./mm10/genome -1  filename_cutadpt_1.fq.gz -2 filename_cutadapt_2.fq.gz -S result.sam
samtools view  -Sb result.sam | samtools sort - -o result_sorted.bam
htseq-count -f bam result_sorted.bam gencode.vM2.annotation.gtf > output.txt
Genome_build: mm10
Supplementary_files_format_and_content: output from htseq-count

source_name: liver

extract_protocol:
Total RNA from liver tissue was extracted by using a mirVana miRNA extraction Kit (Ambion, Austin, TX, USA) according to the manufacturer’s instruction.
1) Filter Small RNA: Separate RNA segment of different size by PAGE gel,select 18-30nt stripe and recycle. 2) Adaptor  ligation: Prepare connection system, blend and centrifuge, connect warmly for a period of time. 3) RT-PCR: Prepare  reverse transcription system, connect warmly for a period on PCR on PCR instrument, then PCR amplification. 4) Purify  PCR products: Recover the Purified PCR construct by PAGE gel, dissolve the recylced products in EB solution. Finally,  label to finish the library construction. 5) Library quality testing: Use Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-  TimePCR System to test quality and production of the prepared library.

treatment_protocol: Excision of liver tissue

value: hepatocellular carcinoma

value: liver

value: 12 weeks


title: HAP1 ARID2KO_SMARCA4dTAG_F5 dTAG 47 3h_2

value: 3h 300 nM dTAG47


title: HAP1 ARID2KO_SMARCA4dTAG_F5 dTAG 47 6h_2

value: 6h 300 nM dTAG47


title: 1a R1 SET WT ESCs rep 1

value: Embryonic stem cells

value: Wt


title: N1611082


title: N1609291


title: sequencing of CGA-2-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat3

description:
SerCGAsgRNA_d4_CGA-2-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: WI38 fast

tag: icas9 induction

tag: the sequenced trna gene

value: repeat 3


title: DIAR STZ 12w liver 36


title: HAP1 ARID2KO_SMARCA4dTAG_F5 dTAG 47 24h_2

value: 24h 300 nM dTAG47


title: DIAR STZ 12w liver 39


title: sequencing of CGA-2-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat1

description:
SerCGAsgRNA_d4_CGA-2-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: iCas9 - SerCGA sgRNA

value: Day 4

tag: repeat


title: HAP1 ARID2KO_SMARCA4dTAG_F5 dTAG 47 72h_2

value: 72h 300 nM dTAG47


title: N1609261

value: salivary glands

value: non-pSS


title: DIAR STZ 10w liver 33

value: 10 weeks


title: N1608181


title: sequencing of CGA-1-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat3

description:
SerCGAsgRNA_d4_CGA-1-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: HAP1 ARID2KO_SMARCA4dTAG_F5 DMSO_2

value: ARID2 KO

value: SMARCA4 dTAG

value: DMSO


title: HAP1 SMARCC2 KO DMSO_1

value: SMARCC2 KO


title: DIAR STZ 6w liver 28

value: hepatocellular carcinoma

value: liver

value: 6 weeks


title: sequencing of CGA-1-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat1

description:
SerCGAsgRNA_d4_CGA-1-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: HAP1 SMARCC1 KO DMSO_1

value: SMARCC1 KO


title: DIAR STZ 6w liver 27


title: sequencing of CGA-1-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat2

description:
SerCGAsgRNA_d4_CGA-1-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: WI38 fast

value: repeat 2


title: sequencing of CGA-2-1 gene in WI38fast-iCas9-SerCGA sgRNA cells, day 4 of iCas9 induction, repeat2

description:
SerCGAsgRNA_d4_CGA-2-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: N1608171


title: HAP1 SMARCA2 KO DMSO_1

value: SMARCA2 KO


title: sequencing of TAG-3-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat3

description:
LeuTAGsgRNA_d8_TAG-3-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

source_name: WI38 fast iCas9 - LeuTAG sgRNA

value: iCas9 - LeuTAG sgRNA

value: Day 8

value: repeat 3


title: HAP1 ARID2 KO DMSO_1


title: DIAR STZ 10w liver 34


title: sequencing of TAG-3-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d8_TAG-3-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: N1609281

value: salivary glands


title: sequencing of TAG-3-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d8_TAG-3-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: sequencing of TAG-2-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat3

description:
LeuTAGsgRNA_d8_TAG-2-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: DIAR control 12w liver 24

value: normal control

value: 12 weeks


title: DIAR STZ 6w liver 26


title: DIAR control 12w liver 23


title: HAP1 SMARCA4 KO DMSO_1

value: SMARCA4 KO


title: DIAR control 12w liver 22


title: DIAR STZ 10w liver 32

value: 10 weeks


title: sc Granuloma annulare patient 1

city: New Haven

first: William

last: Damsky

state: CT

address: 333 Cedar St

institute: Yale School of Medicine

description:
scGA 1
single cell RNA sequencing

data_processing:
Cellranger software suite (v3.1.0) was used to process the scRNAseq data
The Seurat package for R v3.1.5  was used for downstream analysis
Pathway analysis for the entire data set was performed using IPA (Ingenuity Pathway Analysis)
Genome_build: hg38

source_name: Lesional skin

extract_protocol:
4 mm punch biopsies of skin were obtained on separate days from 3 patients with GA and 3 healthy volunteers.. Biopsies were immediately bisected and placed in dispase (10 mg/mL) (Dispase II Sigma Cat# D4693) in RPMI with 2% FBS for 45 minutes at 37°C with shaking at 125 RPM. The tissue was removed from the dispase solution, minced in a sterile plate with a scalpel, and then subsequently incubated with liberase (0.5 mg/mL) (Liberase TH Sigma Cat# 5401135001) in RPMI with 2% FBS for 45 minutes at 37°C with shaking at 125 RPM. The dispase solution was placed on ice. After incubation in the liberase, the dispase solution was combined (to recover any additional cells from the dispase) and the mixture was triturated and filtered through a 100 mM sterile filter. Cells were washed with RPMI + 2% FBS and RBCs were lysed with ACK Lysing Buffer (Lonza Cat# 10-548E) and washed again in RPMI + 2% FBS. Cells were stained with LIVE/DEAD Red viability dye (ThermoFisher Cat# L23102), FC block (Biolegend Cat#422301) and CD45 Alexa Fluor 488 (Biolegend Cat# 304017) in RPMI + 0.1% FBS. Viable cells were isolated using a BD FACS Aria cell sorter and sorted into cold RPMI + 2% FBS. CD45 positivity was recorded but not used as a criterion for sorting. Up to 10,000 cells (depending on yield) were loaded onto a 10X chromium controller for each sample according to the manufacturer’s instructions.
Single cell libraries were created according to the manufacturer’s instructions by the Yale Center for Genome Analysis (YCGA).
Single cell RNA sequencing

value: Skin

value: Granuloma annulare patient


title: sequencing of TAG-2-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d8_TAG-2-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: HAP1 SMARCA4KO_SMARCA2dTAG_C8 dTAG 47 2h_1

value: SMARCA2 dTAG

value: 2h 300 nM dTAG47


title: HAP1 WT DMSO_1

value: wild-type


title: sc Granuloma annulare patient 2

description:
scGA 2
single cell RNA sequencing


title: DIAR control 10w liver 20

value: liver


title: DIAR control 10w liver 18


title: DIAR control 10w liver 17


title: sequencing of TAG-2-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d8_TAG-2-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: WI38 fast


title: sequencing of TAG-1-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d8_TAG-1-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: repeat 2


title: sc Granuloma annulare patient 3

description:
scGA 3
single cell RNA sequencing


title: DIAR control 6w liver 15

value: 6 weeks


title: HAP1 SMARCA4KO_SMARCA2dTAG_C8 dTAG 47 3h_1

value: 3h 300 nM dTAG47


title: sequencing of TAG-1-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d8_TAG-1-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: iCas9 - LeuTAG sgRNA

value: Day 8


title: HAP1 SMARCA4KO_SMARCA2dTAG_C8 dTAG 47 24h_1

value: 24h 300 nM dTAG47


title: DIAR control 6w liver 12

value: normal control


title: Granuloma annulare patient 5 after treated with tofacitinib for six months

data_processing:
Reads were aligned using HISTAT2 (version 2.1.0) against the Genome Reference Consortium Human Build 38 (hg38)
Quantification was done using RefSeq Transcripts release 93.
Quantified reads were normalized to log2(FPKM+1
Differentially expressed genes between control, pre-treatment, and during treatment groups, was carried out on Qlucore Omics Explorer (version 3.5, Qlucore AB, Lund, Sweden)
Pathway analysis for the entire data set was performed using IPA (Ingenuity Pathway Analysis)
Genome_build: hg38

extract_protocol:
Total RNA was extracted with Qiagen RNeasy Fibrous Tissue Mini kits (Qiagen cat# 74704) according to the manufacturer’s instructions. Homogenization of the tissue was achieved using a rotor-homogenizer (PowerGen 125, ThermoFisher). .
RNA was submitted to the Yale Stem Cell Center and complementary DNA libraries were prepared and 100-base pair paired-end stranded sequencing was performed on an Illumina HiSeq 4000, also at Yale Stem Cell Center

treatment_protocol: Five patients with severe, long-standing GA were enrolled and treated with tofacitinib monotherapy (5 mg twice daily) for 6 months; concomitant use of topical or other medications for GA was not permitted

value: after 6 months tofacitinib treatment


title: Granuloma annulare patient 5 prior to treated with tofacitinib

value: before tofacitinib treatment


title: sequencing of TAG-3-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat3

description:
LeuTAGsgRNA_d4_TAG-3-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: Day 4

value: repeat 3


title: HAP1 SMARCA4KO_SMARCA2dTAG_C8 dTAG 47 6h_1

value: SMARCA4 KO

value: 6h 300 nM dTAG47


title: Granuloma annulare patient 4 after treated with tofacitinib for six months

value: Skin

value: Granuloma annulare patient


title: DIAR control 6w liver 11

value: liver


title: sequencing of TAG-3-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d4_TAG-3-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: WI38 fast


title: Granuloma annulare patient 4 prior to treated with tofacitinib


title: Granuloma annulare patient 3 after treated with tofacitinib for six months


title: sequencing of TAG-3-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d4_TAG-3-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: Y1703072

value: salivary glands

value: pSS


title: Granuloma annulare patient 3 prior to treated with tofacitinib


title: sequencing of TAG-2-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat3

description:
LeuTAGsgRNA_d4_TAG-2-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: sequencing of TAG-1-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 8 of iCas9 induction, repeat3

description:
LeuTAGsgRNA_d8_TAG-1-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: Murine heart tissue from infected mice, day 35, control-treated [S_44]

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

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: strain

tag: time of infection

tag: agent

value: Borrelia burgdorferi

value: Control


title: Murine heart tissue from infected mice, day 35, 3-PO-treated [S_54]

tag: treatment


title: HAP1 SMARCC1KO_SMARCC2dTAG_F1 dTAG 47 2h_1

value: SMARCC1 KO

value: SMARCC2 dTAG

value: 2h 300 nM dTAG47


title: HAP1 SMARCA4KO_SMARCA2dTAG_C8 dTAG 47 72h_1

value: SMARCA2 dTAG

value: 72h 300 nM dTAG47


title: HAP1 SMARCC1KO_SMARCC2dTAG_F1 dTAG 47 3h_1

value: 3h 300 nM dTAG47


title: HAP1 SMARCC1KO_SMARCC2dTAG_F1 dTAG 47 24h_1

value: 24h 300 nM dTAG47


title: Murine heart tissue from infected mice, day 35, control-treated [S_43]


title: Granuloma annulare patient 1 prior to treated with tofacitinib

value: before tofacitinib treatment

tag: disease state


title: sequencing of TAG-2-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d4_TAG-2-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: iCas9 - LeuTAG sgRNA

value: Day 4


title: sequencing of TAG-2-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d4_TAG-2-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: repeat 2


title: Murine heart tissue from infected mice, day 35, 3-PO-treated [S_52]


title: Murine heart tissue from infected mice, day 35, 3-PO-treated [S_51]


title: HAP1 SMARCA4KO_SMARCA2dTAG_C8 DMSO_1

value: SMARCA4 KO

value: DMSO


title: Granuloma annulare patient 2 after treated with tofacitinib for six months

value: after 6 months tofacitinib treatment

tag: tissue

value: Skin

value: Granuloma annulare patient


title: Granuloma annulare patient 2 prior to treated with tofacitinib


title: sequencing of TAG-1-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat3

description:
LeuTAGsgRNA_d4_TAG-1-1_WI38fast_rep3
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: WI38 fast

value: repeat 3


title: sequencing of TAG-1-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat2

description:
LeuTAGsgRNA_d4_TAG-1-1_WI38fast_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv


title: Murine heart tissue from infected mice, day 35, control-treated [S_41]

value: Borrelia burgdorferi

value: Control


title: Granuloma annulare patient 1 after treated with tofacitinib for six months


title: Murine heart tissue from infected mice, day 35, 3-PO-treated [S_53]


title: HAP1 SMARCC1KO_SMARCC2dTAG_F1 dTAG 47 72h_1

value: SMARCC1 KO

value: SMARCC2 dTAG


title: HAP1 WT SMARCA4dTAG_F1 dTAG 47 3h_1

value: wild-type

value: SMARCA4 dTAG

value: 3h 300 nM dTAG47


title: sequencing of TAG-1-1 gene in WI38fast-iCas9-LeuTAG sgRNA cells, day 4 of iCas9 induction, repeat1

description:
LeuTAGsgRNA_d4_TAG-1-1_WI38fast_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedWI38fast_allRep.csv

value: iCas9 - LeuTAG sgRNA


title: HAP1 WT SMARCA4dTAG_F1 dTAG 47 2h_1

value: 2h 300 nM dTAG47


title: Murine heart tissue from infected mice, day 35, control-treated [S_40]


title: HAP1 SMARCC1KO_SMARCC2dTAG_F1 DMSO_1


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

description:
nosgRNA_d12_TCG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

source_name: HeLa iCas16

value: HeLa

value: Day 12

value: repeat 2


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

description:
nosgRNA_d12_TCG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

source_name: HeLa iCas15


title: HAP1 SMARCC1KO_SMARCC2dTAG_F1 dTAG 47 6h_1

value: 6h 300 nM dTAG47


title: HAP1 WT SMARCA4dTAG_F1 dTAG 47 24h_1

value: 24h 300 nM dTAG47


title: Murine heart tissue from infected mice, day 56 [S_38]


title: FGF2_11

first: Ronghu

last: Ke

address: No.12 Road WU Nu Mu Qi

institute: Fudan University

data_processing:
Reads cleaning: raw FASTQ files were quality checked using FASTQC . Then fastp was used to quality trim FASTQ files by both read quality and length (Q30 > 20, length > 36).
Alignment: clean reads were processed to pseudo-align to human transcriptome GRCh38 using salmon.
Quantification: transcriptional level expression was aggregated to gene level expression using tximport. Ensembl release 95 was used to annotate genes.
Quality check: sample clustering was performed with principle component analysis analysis and sample to sample distance correlation analysis.
DEGs analysis: differential expressed genes were defined by DESeq2 with foldchange > 2 and adjusted p-value < 0.05. DEGs based hypergeometric test and gene set enrichment analysis were produced by clusterProfiler.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene expression raw counts.csv

source_name: Human dermal fibroblasts

extract_protocol:
Sangon RNA extraction kit (Order NO. B511321)
RNA libraries were prepared for sequencing using TrueSeq standard Illumina protocols

treatment_protocol: Human dermal fibroblasts were cultured in the absence or presence of 4 ng/mL of FGF2 for 48 h. Then, the total RNA was extracted for sequencing.

tag: cell type

value: FB


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

description:
nosgRNA_d12_TAG-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

source_name: HeLa iCas14


title: HAP1 WT SMARCA4dTAG_F1 dTAG 47 6h_1


title: FGF2_8


title: Control3

value: PBS


title: Murine heart tissue from infected mice, day 56 [S_37]


title: FGF2_10


title: Murine heart tissue from infected mice, day 56 [S_39]


title: FGF2_9


title: Control2


title: Murine heart tissue from infected mice, day 56 [S_36]


title: HAP1 WT SMARCA4dTAG_F1 DMSO_1

value: DMSO


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

description:
nosgRNA_d12_CGG-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

source_name: HeLa iCas12


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

description:
nosgRNA_d12_CGA-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

source_name: HeLa iCas10


title: HAP1 ARID2KO_SMARCA4dTAG_F5 dTAG 47 2h_1

value: ARID2 KO


title: Control1


title: Murine heart tissue from infected mice, day 56 [S_35]

value: Borrelia burgdorferi


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

description:
nosgRNA_d12_CGG-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

source_name: HeLa iCas11


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

description:
nosgRNA_d12_CGA-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

source_name: HeLa iCas9


title: HAP1 ARID2KO_SMARCA4dTAG_F5 dTAG 47 6h_1


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

description:
nosgRNA_d12_TAG-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

source_name: HeLa iCas13


title: HAP1 ARID2KO_SMARCA4dTAG_F5 dTAG 47 3h_1


title: HAP1 ARID2KO_SMARCA4dTAG_F5 dTAG 47 24h_1


title: RNA Pol II ChIPseq_rep2

city: San Diego

first: George

last: Sen

state: CA

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Raw ChIP-seq reads were aligned using bwa 0.7.13.
MACS2 (version 2.2.4) was used for call peaks in individual replicates using Input ChIP-seq as the control sample.
Peaks overlapped or IDR peaks among all replicates were obtained using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: bed file with peak data

source_name: Human epidermal keratinocyte

growth_protocol: Primary keratinocytes were grown on culture dishes in keratinocyte EPILIFE medium (Life technologies).

extract_protocol:
10 million cells were crosslinked with 2mM DSG and 1% formaldehyde in the experiment. The ChIP experiment was done using the Lab ChIP-seq protocol, DNA was isolated with Thermo Scientific's GeneJET Gel Extraction kit
ChIP-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

value: keratinocyte

value: undifferentiated keratinocytes

tag: timepoints


title: RNA Pol II ChIPseq_rep1


title: Murine heart tissue from infected mice, day 56 [S_34]


title: Input_ChIPseq


title: ELL_ChIPseq_rep2


title: HAP1 WT SMARCA4dTAG_F1 dTAG 47 72h_1

tag: genotype/variation

value: wild-type

value: 72h 300 nM dTAG47


title: Murine heart tissue from infected mice, day 56 [S_33]


title: Murine heart tissue from infected mice, day 56 [S_32]


title: ELL_ChIPseq_rep1


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

description:
SerCGAsgRNA_d12_CGA-4-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

source_name: HeLa iCas9 - SerCGA sgRNA

value: iCas9 - SerCGA sgRNA


title: Murine heart tissue from infected mice, day 56 [S_31]


title: Murine heart tissue from infected mice, day 56 [S_29]


title: HAP1 ARID2KO_SMARCA4dTAG_F5 dTAG 47 72h_1

tag: dtag

value: SMARCA4 dTAG


title: RNA_Th2KO_96h_rep2

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

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

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.

value: Primary splenic CD4 T cells

tag: time

tag: differentiation

tag: genotype

value: Cxxc1fl/fl CD4-Cre+

tag: stimulation

value: regular

tag: in vitro, in vivo

value: in vitro


title: HAP1 ARID2KO_SMARCA4dTAG_F5 DMSO_1


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

description:
SerCGAsgRNA_d12_CGA-4-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv

tag: cell line

value: HeLa

tag: crispr construct

tag: icas9 induction

value: Day 12

tag: the sequenced trna gene


title: RNA_Th2KO_96h_rep1

tag: strain


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

description:
SerCGAsgRNA_d12_CGA-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

tag: repeat

value: repeat 2


title: Murine heart tissue from infected mice, day 56 [S_30]

tag: time of infection

tag: agent

tag: treatment


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

description:
SerCGAsgRNA_d12_CGA-3-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


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

description:
SerCGAsgRNA_d12_CGA-3-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: Murine heart tissue from infected mice, day 21 [S_16]


title: RH30-ctrl-H3K36me3-002

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
ChIP-seq raw reads were first trimmed low-quality ends using trim-galore (0.4.4; default parameter) and then aligned to the human reference genomes (hg19) using BWA (version 0.7.12; default parameter) and duplicated reads were then marked with Picard (version 1.65), with only nonduplicated reads kept by samtools (version 1.3.1, parameter ‘‘-q 1 -F 1024’’. For data quality control and to estimate the fragment size, the nonduplicated version of SPP (version 1.11) was used to calculate the relative strand correlation value with support of R (version 3.5.1). To visualize ChIP-seq data on the integrated genome viewer (IGV) (version 2.3.82), we utilized genomeCoverageBed (bedtools 2.25.0) to obtain genome-wide coverage in BEDGRAPH file format and then converted it to bigwig file format by bedGraphToBigWig. The bigwig files were scaled to 15 million reads to allow comparison across samples.
MACS2 (version 2.1.1 20160309) was used to call narrow peaks with option “nomodel” and “extsize” defined as fragment size estimated by SPP and a FDR corrected p-value cutoff of 0.05. SICER (version 1.1, with parameters of redundancy threshold 1, window size 200 bp, effective genome fraction 0.86, gap size 600 bp, FDR 0.00001 with fragment size defined above) was used for broad peak/domain calling. Enriched regions were identified by comparing the ChIP library file to input library file. Peak regions were defined to be the union of peak intervals from ChIP replicates. Genomic feature annotation of peaks was carried out by annotatePeaks.pl, a program from HOMER suite (v4.8.3, http://homer.salk.edu/homer/).
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: bigwig

growth_protocol: Rh30 were cultured in RPMI medium, supplemented with 10% FBS, and 100 U/mL penicillin/streptomycin.

extract_protocol:
RH30 cells 10 millions with DMSO control or Geldanamycin 1µM treatment for 24 h were cross-linked with fresh prepare 1% formaldehyde (final concentration) for 10 min and quenched with 125 mM glycine for 5 min at room temperature. Cells were washed once with Dulbecco's Phosphate-Buffered Saline (DPBS). Cell lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40 with 1 tablet protease inhibitor cocktail) were added to plate after aspirate DPBS and add 5-8 ml cold (4°C). The cells were scraped with a cell scraper and transfer into 50-ml conical tubes on ice.  Cell pellets were collected by centrifuging at 2,000 rpm for 5 minutes at 4°C. The pellets were resuspended in cell lysis buffer and incubated on ice for 10 min. Cells were passed through a 20-gauge needle 20 times. The nuclei were collected by centrifuging at 2,000 rpm at 4°C for 5 minutes. The nuclear pellets were resuspended and lysed with 250 μl RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS with 1 tablet protease inhibitor cocktail). The lysates were sonicated for at least 30 min (30 sec on / 30 sec off) using Bioruptor Pico (Diagenode, Inc., Denville, NJ) and centrifuged at 14,000 rpm in a microfuge for 15 minutes at 4°C. The supernants were collected and sonicated DNA fragments were examined by electrophoresis on a 1% agarose gel. The sonicated samples with enrichment of fragments in the 100 to 500 bp range will be used for the chromatin immunoprecipitation (Chip) after remove 50 μL from each sample as input. The primary antibodies H3K9me3 (Millipore, 07-442) and H3K36me3 (RevMab, 31-1051-00) were coupled with 25 μL magnetic beads (Dynabeads M-280 Sheep Anti-Rabbit IgG, Invitrogen 11203D) overnight in the cold room at 4°C. The primary antibody coupled magnetic beads were washed three times with PBS/BSA (1XPBS / 5 mg/ml BSA (fraction V)) at 4°C, then incubated with sonicated DNA chromatin samples overnight in the cold room at 4°C. The beads containing immuno-bound chromatin were collected by placing the microfuge tube on a magnet rack. The beads were extensively washed with LiCl wash buffer (100 mM Tris pH 7.5 / 500 mM LiCl / 1% NP-40 / 1% sodium deoxycholate) 5 times and TE Buffer (10 mM Tris-HCl pH 7.5 / 0.1 mM Na2EDTA) once. Bound chromatin was eluted by IP Elution Buffer (1 % SDS / 0.1 M NaHCO3) and reverse-crosslinked at 65°C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen, Valencia, CA) after the treatment of RNase A and proteinase K.
5-10 ng of DNA was using to prepare libraries by the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext Q5 Hot Start HiFi PCR Master Mix according to the manufacturer’s instructions (New England Biolabs). Completed ChIP-seq libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (Perkin Elmer). All libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies), Kapa Library Quantification kit (Kapa Biosystems).

treatment_protocol: Rh30 cells were treated with Geldanamycin 1µM or DMSO 0.1% for 24h.

tag: cell type

tag: antibody


title: RH30-ctrl-H3K9me3-001

value: Millipore, 07-442


title: RH30-ctrl-H3K36me3-001

value: DMSO


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

description:
SerCGAsgRNA_d12_CGA-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: RNA_Th2KO_48h_rep2


title: RH30-ctrl-H3K9me3-002


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

description:
SerCGAsgRNA_d12_CGA-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: RNA_Th2KO_120h_rep1


title: RNA_Th2KO_48h_rep1


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

description:
SerCGAsgRNA_d12_CGA-1-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: RNA_Th2KO_120h_rep2


title: RH30-ctrl-input-002


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

description:
SerCGAsgRNA_d8_CGA-4-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: Day 8


title: Murine heart tissue from infected mice, day 21 [S_13]

value: Borrelia burgdorferi


title: RH30-Gel-H3K36me3-002

value: Geldanamycin 1 uM


title: Murine heart tissue from infected mice, day 21 [S_14]


title: RH30-ctrl-input-001


title: Murine heart tissue from infected mice, day 21 [S_12]


title: RNA_Th2KO_0h_rep2

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


title: Murine heart tissue from infected mice, day 21 [S_11]


title: RH30-Gel-H3K36me3-001


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

description:
SerCGAsgRNA_d8_CGA-3-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: Murine heart tissue from infected mice, day 7 [S_09]


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

description:
SerCGAsgRNA_d8_CGA-4-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: Murine heart tissue from infected mice, day 21 [S_15]


title: RNA_Th2KO_0h_rep1


title: Murine heart tissue from infected mice, day 7 [S_10]


title: RNA_Th2_96h_rep2

value: WT


title: Murine heart tissue from infected mice, day 7 [S_07]


title: RNA_Th2_96h_prolong_rep2

value: prolong


title: Murine heart tissue from infected mice, day 7 [S_08]


title: RNA_Th2_96h_rep1


title: RH30-Gel-H3K9me3-002


title: RNA_Th2_96h_prolong_rep1


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

description:
SerCGAsgRNA_d8_CGA-3-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: RH30-Gel-input-002


title: RH30-Gel-H3K9me3-001


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

description:
SerCGAsgRNA_d8_CGA-1-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv


title: Murine heart tissue from infected mice, day 7 [S_06]


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

description:
SerCGAsgRNA_d8_CGA-2-1_HeLa_rep1
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep1.csv


title: Murine heart tissue from infected mice, day 7 [S_05]


title: RNA_Th2_48h_rep2


title: Murine heart tissue from infected mice, uninfected control [S_04]


title: control 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

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

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: genotype/variation

value: control


title: RH30-Gel-input-001


title: Murine heart tissue from infected mice, uninfected control [S_02]


title: control rep2


title: RNA_Th2_48h_rep1

tag: time


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

description:
SerCGAsgRNA_d8_CGA-2-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: iCas9 - SerCGA sgRNA


title: RNA_Th2_48h_prolong_rep1

tag: differentiation


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

description:
SerCGAsgRNA_d4_CGA-4-1_HeLa_rep2
processed data file: genomictRNAseq_CRISPResso_tRNAtargetedHeLa_Rep2.csv

value: Day 4