title: SPF_bulkRNAseq_MMRintCD11c+CD9hiCD121b+ rep2

city: Bethesda

first: Byunghyun

last: Kang

state: Maryland

address: 9000 Rockville Pike

institute: NIAID

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3570-L1_H3VKTBGX7_S13

data_processing:
Basecalls performed using CASAVA version 2.0
For scRNAseq analysis, read alignment and generation of digital gene data from raw sequence data were performed using STAR v2.5.4a with default settings and drop-seq-tools-1.12. Data were aligned to the Mus musculus (mm10) genome and annotated using USCS mm10 gene annotation. The tagged cell barcode and UMI information was mapped again into aligned/annotated sequences, followed by bead synthesis error correction and digital gene expression extraction (DGE).
The downstream analysis of demultiplexed bulkRNAseq fastq files was executed using Partek Flow (Partek): trimming adaptor sequences (13bp from 5’ and 3bp from 3’ were trimmed, leaving 57~58bp with higher than Q30 of quality score in average), alignment to the reference genome (mm10), and quantification to annotation model (mm10_refseq_v86_18_08_01_v2). STAR aligner was used for sequence alignment and the genomic alignments that map uniquely to the set of known Refseq were used as raw input. TPM normalized count matrix was exported for further secondary analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI counts for scRNAseq and TMP normalized values for bulkRNAseq

source_name: colon macrophages

extract_protocol:
Single cell suspensions of colon LP cells were prepared from mouse colons of 10-15 pooled 7-10 weeks-old SPF or GF mice for scRNA-seq or from pooled colons of 3-5 SPF or GF mice for bulk RNA-seq. Target cells were FACs-sorted and immediately moved to capture cells within oil-droplets by single cell or 100 cells of target cells were directly sorted into 96 well PCR plate containing ~10ul of reaction buffer from SMART-Seq v4 Ultra Low Input RNA Kit (Takara).
All the rest procedures following single cell encapsulation were performed according to the standard Drop-seq protocol. The amplified cDNA was quantified on Qubit 2.0 and BioAnalyzer 2100 with DNA high-sensitivity chip (Agilent) and then fragmented and amplified using the Nextera XT DNA sample prep kit (Illumina). Final libraries were again quantified on Qubit 2.0 and assessed for fragment size and quality using the BioAnalyzer 2100 with a DNA high-sensitivity chip (Agilent).
To generate bulk RNAseq libraries from the sorted 100 cells, first-strand cDNA synthesis and PCR amplification were carried out according to the protocol of SMART-Seq v4 Ultra Low Input RNA Kit. Tagmentation and indexing of the amplified cDNAs were performed using the Nextera XT library preparation kit (Illumina) with multiplexing primers, according to manufacturer’s protocol.

tag: strain

tag: tissue

value: colon

value: specific pathogen free

value: 8-12 weeks


title: GF_bulkRNAseq_MMRintCD11c-CD9+CCR2- rep1

status: Public on Sep 25 2019

type: SRA

country: USA

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3549-L1_H2NWFBGX7_S8

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: germ-free

tag: age


title: GF_bulkRNAseq_CD11b+MHCII-Lin-Ly6chi rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3560-L1_H3VKTBGX7_S3


title: SPF_bulkRNAseq_MMRintCD11c-CD9-CCR2+ rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3572-L1_H3VKTBGX7_S15


title: SPF_bulkRNAseq_MMRhiLYVE1-CD169+CD11c- rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3566-L1_H3VKTBGX7_S9


title: GF_bulkRNAseq_MMRintCD11c-CD9-CCR2+ rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3564-L1_H3VKTBGX7_S7


title: GF_bulkRNAseq_MMRhiLYVE1-CD169+CD11c- rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3558-L1_H3VKTBGX7_S1


title: GF_bulkRNAseq_MMRintCD11c-CD9-CCR2+ rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3548-L1_H2NWFBGX7_S7


title: GF_bulkRNAseq_MMRintCD11c+CD9hiCD121b+ rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3562-L1_H3VKTBGX7_S5


title: SPF_bulkRNAseq_MMRhiLYVE1+CD169+CD11c- rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3567-L1_H3VKTBGX7_S10


title: GF_bulkRNAseq_MMRhiLYVE1+CD169+CD11c- rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3559-L1_H3VKTBGX7_S2


title: SPF_bulkRNAseq_CD11b+MHCII-Lin-Ly6chi rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3568-L1_H3VKTBGX7_S11


title: SPF_bulkRNAseq_MMRintCD11c+CD9hiCD121b- rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3571-L1_H3VKTBGX7_S14


title: GF_bulkRNAseq_MMRintCD11c+CD9hiCD121b- rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3563-L1_H3VKTBGX7_S6


title: SPF_bulkRNAseq_MMRintCD11c-CD9+CCR2- rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3573-L1_H3VKTBGX7_S16


title: SPF_bulkRNAseq_MMRintCD11c-CD9-CCR2+ rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3556-L1_H2NWFBGX7_S15


title: SPF_bulkRNAseq_MMRintCD11c-CD9+CCR2- rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3557-L1_H2NWFBGX7_S16


title: GF_bulkRNAseq_MMRintCD11c+CD9hiCD121b- rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3547-L1_H2NWFBGX7_S6


title: SPF_bulkRNAseq_MMRintCD11c+CD9hiCD121b- rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3555-L1_H2NWFBGX7_S14


title: SPF_bulkRNAseq_MMRintCD11c+CD9hiCD121b+ rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3554-L1_H2NWFBGX7_S13


title: GF_bulkRNAseq_MMRintCD11c-CD9+CCR2- rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3565-L1_H3VKTBGX7_S8


title: SPF_bulkRNAseq_CD11b+MHCII+Lin-Ly6chi rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3569-L1_H3VKTBGX7_S12


title: GF_bulkRNAseq_CD11b+MHCII+Lin-Ly6chi rep2

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3561-L1_H3VKTBGX7_S4


title: SPF_bulkRNAseq_CD11b+MHCII+Lin-Ly6chi rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3553-L1_H2NWFBGX7_S12


title: GF_bulkRNAseq_MMRhiLYVE1+CD169+CD11c- rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3543-L1_H2NWFBGX7_S2


title: GF_bulkRNAseq_CD11b+MHCII-Lin-Ly6chi rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3544-L1_H2NWFBGX7_S3


title: SPF_bulkRNAseq_CD11b+MHCII-Lin-Ly6chi rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3552-L1_H2NWFBGX7_S11


title: SPF_bulkRNAseq_MMRhiLYVE1+CD169+CD11c- rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3551-L1_H2NWFBGX7_S10


title: GF_bulkRNAseq_CD11b+MHCII+Lin-Ly6chi rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3545-L1_H2NWFBGX7_S4


title: GF_bulkRNAseq_MMRhiLYVE1-CD169+CD11c- rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3542-L1_H2NWFBGX7_S1

value: 7-10 weeks


title: GF_scRNAseq

description: gf_colon_phagocytes_Dropseq_UMI_raw_counts.txt

source_name: colon macrophages and dendritic cells


title: MC38-OVA 1

city: Daejeon

first: Chang Gon

last: Kim

address: 291 Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
MC38-OVA
MC38-OVA 1.txt

data_processing:
Alignment: Bowtie2 (for RNA-seq)
Assembly: EdgeR (for RNA-seq)
Additional processing: abundance measurement (for RNA-seq)
Mapping: BWA-mem (for ChIP-seq)
Filtering: reads with MAPQ < 10 were removed, PCR duplicates were removed by Picard
Additional processing: ChIP peaks were identified by MACS
Genome_build: hg38, mm9
Supplementary_files_format_and_content: Normal colon 1/2/3, MC38-OVA 1/2/3: raw read counts (.txt)  Control siRNA specific peaks: specific peaks in H3K27ac ChIP-seq in control siRNA-transfected CD8+ T cells

source_name: Tissue

extract_protocol: H3K27ac was purified with anti-H3K27ac antibody and RNA was extracted from cells using TRIZOL reagent.

tag: harvest time

value: 14 days after implantation

tag: treatment

value: No treatment


title: TSC_RNAseq_KD_Zfpm1_day3

city: Austin

first: Bum-Kyu

last: Lee

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

description:
RNAseq of Zfpm1 KD in dTSCs (d3)
RNAseq.expression.TPM.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse mm9 genome using bowtie2 for ChIP-seq and ATAC-seq. Salmon was used for mapping reads of RNA-seq.
Peaks of ChIP-seq and ATAC-seq were called using MACS peak caller. Tximport was used for calculating TPM for RNA-seq.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-seq and ATAC-seq, tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak. For RNA-seq, one tab-delimited text file contains all RNA-seq data. Gene expression was shown as TPM values for each genes.

source_name: Trophoblast stem cells

growth_protocol: Mouse J1 ES cells were cultivated in 0.1% gelatin coated dishes using DMEM (Dulbecco’s modified Eagle’s medium) supplemented with 15% fetal bovine serum (FBS), 2 mM of L-glutamine, 0.1 mM of non-essential amino acid, 1% of nucleoside mix, 0.1 mM of ß-mercaptoethanol, 1000U/ml of recombinant leukemia inhibitory factor and 50 U/ml of Penicillin/Streptomycin. Mouse trophoblast stem cells (TSCs) were maintained in TS cell culture media (mixture of mouse embryonic fibroblast (MEF)-conditioned TS medium with TS basal medium at a ratio of 3:7) supplemented with 25ng/ml Fgf4 and 1ug/ml of heparin. The TS basal medium is composed of RPMI 1640 medium (Gibco) supplemented with 20% FBS, 100 mM β-mercaptoethanol, 2 mM L-glutamine, 1 mM sodium pyruvate, 50 U/mL penicillin/streptomycin.

extract_protocol:
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution in J1 mouse ES cells. Briefly, cells were cross-linked with 1% formaldehyde for 7 min at room temperature, and then formaldehyde was quenched by adding glycine (final 125 mM) for 5 min. After washing cells with PBS two times, fixed cell pellets were resuspended in ChIP dilution buffer and sonicated using a Bioruptor (Diagenode) with a setting of 30 sec on and 1 min off for 10 min (3 times). Sheared chromatins containing average size of 300 bp DNA fragments were used for immunoprecipitation using 10ug of a native antibody against each factor. Immunoprecipitated DNA was sequenced using Illumina sequencers. Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) was performed in in both ESCs and TSCs. Briefly, tagmentation reaction was performed with 50ng of target DNA, and then bPCR-compatible sites and barcode were added into the target DNA by PCR. After cleaning up the PCR products using Zymo DNA clean and concentrator-5 kit, the final product was sequenced using Illumina NextSeq 500 machine. Global gene expression profiles using RNA-seq were performed in both ESCs and TSCs.  Briefly, total RNAs were isolated using the RNeasy plus minikit (Qiagen). mRNAs were enriched from total RNAs, fragmented, and primed. First strand cDNAs were synthesized following by second strand synthesis. The ends of purified double strand cDNAs were repaired, ligated with a barcoded adaptor, and amplified with PCR. Purified final PCR product was sequenced using Illumina NextSeq 500 machine.
ChIP-seq library  was constructed using the NEB ChIP-seq library prep. kit (E6200L ) following by manufacturer’s instructions. ATAC-seq library was constructed using Nextera DNA library prep kit following the manufacturer’s protocol. RNA-seq library was constructed using NEBNext Ultra RNA Library prep kit (NEB, E7530S) according to manufacturer’s instruction

treatment_protocol: To differentiate TSCs, They were cultivated in TS basal medium without Fgf4 and heparin

tag: cell type

value: mouse embryonic stem cells

value: TS3.5 TS cells


title: GF_bulkRNAseq_MMRintCD11c+CD9hiCD121b+ rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3546-L1_H2NWFBGX7_S5


title: MC38-OVA 2

description:
MC38-OVA
MC38-OVA 2.txt


title: ESC_RNAseq_rep1

description:
RNA-seq of ES cells
RNAseq.expression.TPM.txt

source_name: Embryonic stem cells

extract_protocol:
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution in J1 mouse ES cells. Briefly, cells were cross-linked with 1% formaldehyde for 7 min at room temperature, and then formaldehyde was quenched by adding glycine (final 125 mM) for 5 min. After washing cells with PBS two times, fixed cell pellets were resuspended in ChIP dilution buffer and sonicated using a Bioruptor (Diagenode) with a setting of 30 sec on and 1 min off for 10 min (3 times). Sheared chromatins containing average size of 300 bp DNA fragments were used for immunoprecipitation using 10ug of a native antibody against each factor. Immunoprecipitated DNA was sequenced using Illumina sequencers. Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) was performed in in both ESCs and TSCs. Briefly, tagmentation reaction was performed with 50ng of target DNA, and then bPCR-compatible sites and barcode were added into the target DNA by PCR. After cleaning up the PCR products using Zymo DNA clean and concentrator-5 kit, the final product was sequenced using Illumina NextSeq 500 machine. Global gene expression profiles using RNA-seq were performed in both ESCs and TSCs.  Briefly, total RNAs were isolated using the RNeasy plus minikit (Qiagen). mRNAs were enriched from total RNAs, fragmented, and primed. First strand cDNAs were synthesized following by second strand synthesis. The ends of purified double strand cDNAs were repaired, ligated with a barcoded adaptor, and amplified with PCR. Purified final PCR product was sequenced using Illumina NextSeq 500 machine.
ChIP-seq library  was constructed using the NEB ChIP-seq library prep. kit (E6200L ) following by manufacturer’s instructions. ATAC-seq library was constructed using Nextera DNA library prep kit following the manufacturer’s protocol. RNA-seq library was constructed using NEBNext Ultra RNA Library prep kit (NEB, E7530S) according to manufacturer’s instruction
ChIP-Seq, ATAC-seq, and RNA-seq

value: J1 ES cells


title: TSC_RNAseq_rep2

description:
RNA-seq of TS cells
RNAseq.expression.TPM.txt

value: mouse trophoblast stem cells


title: SPF_bulkRNAseq_MMRhiLYVE1-CD169+CD11c- rep1

description:
colon_macrophageSubsets_bulkRNAseq_TPM_normalized.txt
AB3550-L1_H2NWFBGX7_S9


title: ESC_RNAseq_rep2


title: TSC_RNAseq_KD_Foxj2_day3

description:
RNAseq of Foxj2 KD in dTSCs (d3)
RNAseq.expression.TPM.txt


title: TSC_RNAseq_KD_Ets2_day3

description:
RNAseq of Ets2 KD in dTSCs (d3)
RNAseq.expression.TPM.txt


title: ESC_ATACseq_rep2

description: ATAC-seq of ES cells

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse mm9 genome using bowtie2 for ChIP-seq and ATAC-seq. Tophat2 was used for mapping reads of RNA-seq.
Peaks of ChIP-seq and ATAC-seq were called using MACS peak caller. Cufflinks was used for counting reads in exons for RNA-seq.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-seq and ATAC-seq, tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak. For RNA-seq, one tab-delimited text file contains all RNA-seq data. Gene expression was shown as log2(FPKM+1) values for each genes.

molecule: genomic DNA


title: TSC_RNAseq_KD_Id2_day3

description:
RNAseq of Id2 KD in dTSCs (d3)
RNAseq.expression.TPM.txt


title: TSC_RNAseq_rep1


title: TSC_ATACseq_rep1

description: ATAC-seq of TS cells


title: TSC_RNAseq_KD_Pcgf5_day3

description:
RNAseq of Pcgf5 KD in dTSCs (d3)
RNAseq.expression.TPM.txt


title: TSC_RNAseq_KD_Hand1_day3

description:
RNAseq of Hand1 KD in dTSCs (d3)
RNAseq.expression.TPM.txt


title: TSC_ATACseq_rep2

description: ATAC-seq of TS cells


title: ESC_ATACseq_rep1

description: ATAC-seq of ES cells


title: dTSC_ChIPseq_Mock_control_rep2

description: Chromatin IP against Mock

tag: chip antibody

value: Mock


title: dTSC_ChIPseq_Pou3f1

description: Chromatin IP against Pou3f1


title: dTSC_ChIPseq_Hopx

description: Chromatin IP against Hopx

value: Hopx


title: dTSC_ChIPseq_Irf2

description: Chromatin IP against Irf2


title: dTSC_ChIPseq_Mafk

description: Chromatin IP against Mafk

value: Mafk


title: dTSC_ChIPseq_Maff

description: Chromatin IP against Maff

value: Maff


title: SPF_scRNAseq

description: spf_colon_phagocytes_Dropseq_UMI_raw_counts.txt


title: TSC_RNAseq_KD_Lrrfip1_day3

description:
RNAseq of Lrrfip1 KD in dTSCs (d3)
RNAseq.expression.TPM.txt


title: dTSC_ChIPseq_Elf5

description: Chromatin IP against Elf5


title: TSC_ChIPseq_cFos

description: Chromatin IP against cFos

value: cFos


title: TSC_ChIPseq_Zfpm1_rep2

description: Chromatin IP against Zfpm1


title: TSC_ChIPseq_Tead4_rep2

description: Chromatin IP against Tead4


title: TSC_ChIPseq_Tead4_rep1

description: Chromatin IP against Tead4


title: TSC_ChIPseq_Pcgf5_rep2

description: Chromatin IP against Pcgf5


title: TSC_ChIPseq_Pcgf5_rep1

description: Chromatin IP against Pcgf5


title: dTSC_ChIPseq_Mock_control_rep1

description: Chromatin IP against Mock


title: TSC_ChIPseq_Pou3f1

description: Chromatin IP against Pou3f1


title: TSC_ChIPseq_Smad6_rep2

description: Chromatin IP against Smad6


title: TSC_ChIPseq_Mock_control_rep2

description: Chromatin IP against Mock


title: TSC_ChIPseq_Tbx20_rep2

description: Chromatin IP against Tbx20


title: TSC_ChIPseq_Tbx20_rep1

description: Chromatin IP against Tbx20


title: TSC_ChIPseq_Meis1

description: Chromatin IP against Meis1


title: TSC_ChIPseq_Mock_control_rep1

description: Chromatin IP against Mock


title: TSC_ChIPseq_Tfap2c

description: Chromatin IP against Tfap2c


title: TSC_ChIPseq_Mef2d_rep2

description: Chromatin IP against Mef2d


title: TSC_ChIPseq_Maff_rep1

description: Chromatin IP against Maff


title: TSC_ChIPseq_Zfpm1_rep1

description: Chromatin IP against Zfpm1


title: TSC_ChIPseq_Med12

description: Chromatin IP against Med12


title: TSC_ChIPseq_Mafk_rep1

description: Chromatin IP against Mafk


title: TSC_ChIPseq_Lrrfip1_rep2

description: Chromatin IP against Lrrfip1


title: TSC_ChIPseq_Maff_rep2

description: Chromatin IP against Maff


title: TSC_ChIPseq_Mafk_rep2

description: Chromatin IP against Mafk


title: TSC_ChIPseq_p300

description: Chromatin IP against p300


title: TSC_ChIPseq_Irf2_rep2

description: Chromatin IP against Irf2


title: TSC_ChIPseq_Id2_rep1

description: Chromatin IP against Id2


title: TSC_ChIPseq_Hpox_rep1

description: Chromatin IP against Hpox

value: Hpox


title: TSC_ChIPseq_Irf2_rep1

description: Chromatin IP against Irf2


title: TSC_ChIPseq_Hopx_rep2

description: Chromatin IP against Hopx


title: TSC_ChIPseq_Mef2d_rep1

description: Chromatin IP against Mef2d


title: TSC_ChIPseq_Hic2_rep1

description: Chromatin IP against Hic2


title: TSC_ChIPseq_H3K4me1_rep3

description: Chromatin IP against H3K4me1


title: TSC_ChIPseq_Hic2_rep2

description: Chromatin IP against Hic2


title: TSC_ChIPseq_H3K27ac_rep1

description: Chromatin IP against H3K27ac


title: TSC_ChIPseq_Lrrfip1_rep1

description: Chromatin IP against Lrrfip1


title: TSC_ChIPseq_H3K4me1_rep2

description: Chromatin IP against H3K4me1


title: TSC_ChIPseq_H3K4me1_rep1

description: Chromatin IP against H3K4me1


title: TSC_ChIPseq_Foxj2_rep1

description: Chromatin IP against Foxj2


title: TSC_ChIPseq_Foxj2_rep2

description: Chromatin IP against Foxj2


title: TSC_ChIPseq_Fbxo21_rep1

description: Chromatin IP against Fbxo21


title: TSC_ChIPseq_Fbxo21_rep2

description: Chromatin IP against Fbxo21


title: TSC_ChIPseq_Ets2_rep2

description: Chromatin IP against Ets2


title: TSC_ChIPseq_Id2_rep2

description: Chromatin IP against Id2


title: TSC_ChIPseq_H3K27ac_rep2

description: Chromatin IP against H3K27ac


title: TSC_ChIPseq_Ets2_rep1

description: Chromatin IP against Ets2


title: TSC_ChIPseq_Eomes_rep2

description: Chromatin IP against Eomes

value: Eomes


title: TSC_ChIPseq_Eomes_rep1

description: Chromatin IP against Eomes


title: TSC_ChIPseq_Elf5

description: Chromatin IP against Elf5


title: TSC_ChIPseq_Smad6_rep1

description: Chromatin IP against Smad6


title: TSC_ChIPseq_Ctcf

description: Chromatin IP against Ctcf

value: Ctcf


title: TSC_ChIPseq_Cbfa2t3_rep2

description: Chromatin IP against Cbfa2t3


title: DCIS_Vector_2

type: RNA

city: Baltimore

first: Saraswati

last: Sukumar

state: MD

address: 1650 Orleans St, CRB 1, Rm 132

department: Breast Cancer Program

institute: Johns Hopkins School of Medicine

description: Gene expression after transfection

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Scanned using Agilent Technologies Scanner G2505C

data_processing: Data was exported using Agilent Feature Extraction. Following that, the data was imported into R and normalized using quantile normalization. ComBat was used for batch correction.

organism: Homo sapiens

source_name: DCIS.COM cells transfected with control vector

label_protocol: Standard Cy3 labeling protocol

growth_protocol: MCF10AT1 and DCIS.COM were obtained from Barbara Ann Karmanos Cancer Institute (Detroit, MI). Cells were authenticated using short tandem repeat (STR) profiling and tested for mycoplasma using MycoAlert PLUS mycoplasma detection kit (# LT07-218, Lonza).

extract_protocol: RNA from MCF10AT1 and DCIS.COM cells overexpressing CRYβB2 or vector control was extracted using RNeasy Mini Kit (Qiagen).

treatment_protocol: MCF10AT1 and DCIS.COM cells overexpressing luciferase and CRYβB2 were generated following lentivirus infection.

tag: cell line

value: breast cancer

tag: vector

value: control

tag: batch


title: 10AT1_CRYBB2_2

description: Gene expression after transfection

source_name: 10AT1 cell lines transfected with CRYBB2


title: TSC_ChIPseq_Creb3l2_rep1

description: Chromatin IP against Creb3l2


title: TSC_ChIPseq_Cbfa2t3_rep1

description: Chromatin IP against Cbfa2t3


title: TSC_ChIPseq_Bhlhe40_rep2

description: Chromatin IP against Bhlhe40


title: 10AT1_CRYBB2_2.1

description: Gene expression after transfection


title: 10AT1_Vector_2

description: Gene expression after transfection

source_name: 10AT1 cell lines transfected with control vector


title: DCIS_Vector_1

description: Gene expression after transfection


title: DCIS_CRYBB2_2

description: Gene expression after transfection

source_name: DCIS.COM cells transfected with CRYBB2


title: 10AT1_CRYBB2_1

description: Gene expression after transfection


title: 10AT1_Vector_2.1

description: Gene expression after transfection


title: TSC_ChIPseq_Bbx_rep2

description: Chromatin IP against Bbx

value: Bbx


title: TSC_ChIPseq_Bhlhe40_rep1

description: Chromatin IP against Bhlhe40


title: TSC_ChIPseq_Creb3l2_rep2

description: Chromatin IP against Creb3l2


title: 10AT1_Vector_1

description: Gene expression after transfection


title: TSC_ChIPseq_Bbx_rep1

description: Chromatin IP against Bbx


title: ESC_ChIPseq_p300

description: Chromatin IP against p300

value: mouse embryonic stem cell


title: CWR22Rv1 ATRX KO clone 2

city: Chicago

first: Mindy

middle: Kim

last: Graham

state: IL

address: 303 E. Superior Street Chicago

department: Urology

institute: Northwestern University Feinberg School of Medicine

description: Gene expression after ATRX KO

hyb_protocol: Agilent human GE 4x 44K v2 microarrays (G4845A) were used, which contain 41,000 unique probes targeting 27,958 Entrez gene RNAs. 0.825 ug of each Cy3-labeled samples was used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol in a walk-in ozone-controlled enclosure.

scan_protocol: Microarrays were scanned using an Agilent G2565A Scanner controlled by Agilent Scan Control 7.0 software. Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

data_processing: All data analysis for DNA was carried out using the R statistical software suite using both standard and customized routines. Agilent expression array data was imported and quantile normalized using functions included in the Limma Bioconductor software package. Finally, expression values were transformed to a log-base-2 scale.  Gene annotations were provided by the array manufacturer.  Differential expression was calculated using Empirical Bayes linear models as implemented in the limma package from Bioconductor. When both cell lines were used together in an analysis, expression values were standardized within cell line, by subtracting the parental transcriptional profile from each ATRX knockout replicate.

source_name: CWR22Rv1 ATRX KO clone 2

label_protocol: Sample amplification and labeling procedures were carried out by using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). ) with minor modifications. Briefly, 0.4 ug total RNA was reverse-transcribed into cDNA by MMLV-RT using an oligo dT primer (System Biosciences) that incorporates a T7 promoter sequence. The cDNA is then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-3 labeled CTP (Perkin Elmer). The labeled cRNA is purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) are added to RNA samples before amplification and labeling according to manufacturer’s protocol.

growth_protocol: LAPC-4 was cultured in Iscove's Modified Dulbecco's Medium (IMDM, Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Sigma), 1% of mixture of Penicillin 10,000 units/mL and Streptomycin 10,000 ug/mL (Pen/Strep, Quality Biological), and 1 nM of R1881. CWR22Rv1 and PC3 were cultured in RPMI 1640 (Gibco) supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol: Total RNA was isolated from cell pallets using TriZol reagent (Invitrogen) followed by RNeasy mini kit with DNase on-column digestion (Qiagen). RNA was quantified with NanoDrop ND-1000 followed by quality assessment with 2100 Bioanalyzer (Agilent Technologies) according to manufacturer’s protocol.

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: Prostate Cancer Cell

tag: gender

value: Male

tag: genotype/variation

value: ATRX KO


title: LAPC-4_ATRX_KO_clone_3

description: Gene expression after ATRX KO

source_name: LAPC-4 ATRX KO clone 3


title: Parental_CWR22Rv2_cell_line

description: Gene expression of parental cell line

source_name: Parental CWR22Rv2 cell line

value: wildtype


title: CWR22Rv1 ATRX KO clone 3

description: Gene expression after ATRX KO

source_name: CWR22Rv1 ATRX KO clone 3


title: LIFRNeg2

city: Cambridge

first: Edwin

middle: Antonio

last: Rosado-Olivieri

state: MA

address: 7 Divinity Ave

department: Department of Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
For single cell RNA-seq data, the Cell Ranger software pipeline (10X Genomics) was used to demultiplex barcodes and map reads to transcriptome.
For bulk RNA-sequencing, reads were trimmed for universal ilumina adapters with Cutadapt v1.8.1 and assessed for quality control using Fastqc v0.11.5. Reads were aligned to the human reference genome (hg38) with Tophat v2.1.1 using default parameters. Downstream transcript quantification and differential gene expression analysis was performed with Cufflinks v2.2.1 (Trapnell et al., 2013).
Genome_build: GRCh38
Supplementary_files_format_and_content: For single cell RNA-seq processed data, feature barcode matrixes are provided in Hierarchical Data Format (.h5). For bulk RNA-seq, a matrix of normalized FPKM gene expression values are included for each sample.

source_name: stem cell-derived beta cells

growth_protocol: Stem cell-derived beta cells were differentiated from HUES8 cell line using a published protocol for the directed differentiation of beta cells (Pagliuca et al., 2014; Cell)

extract_protocol:
Clusters of cells were dispersed and accutase and single cell suspensions were processed for bulk RNA extraction or single cell RNA-sequencing preparatios.
Single cell RNA-Seq libraries were made following standard 10x Chromiun v2 library preparation. Library was sequenced as follows: 26bp Read 1 (16bp Chromium barcode and 10bp UMI), 57bp Read 2 (transcript), and 8bp i7 sample barcode for each scRNA-Seq library. For bulk RNA-sequencing, extracted RNA was processed using SMARTseq v4 kit (Takara) and followed by library preparation using the NexteraXT kit (Illumina).

value: stem cell-derived beta cells

tag: sample type

value: LIFR neg sorted cells

tag: type of sequencing

value: bulk RNA-seq


title: LIFRNeg3


title: LIFRNeg4


title: CWR22Rv1 ATRX KO clone 1

description: Gene expression after ATRX KO

source_name: CWR22Rv1 ATRX KO clone 1


title: LIFRNeg1


title: DCIS_CRYBB2_1

description: Gene expression after transfection


title: LIFRPos4

value: LIFR pos sorted cells


title: TSC_ChIPseq_Arid3a

description: Chromatin IP against Arid3a

value: mouse trophoblast stem cells

value: TS3.5 TS cells


title: LIFRPos3


title: LIFRPos2


title: HeLa_nonCSC, mRNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: HeLa, nonCSC

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: HeLa cells transfected with ZsGreen-cODCdegron were cultured in DMEM supplemented with 10% FBS and 1% P/S.

extract_protocol: ISOGEN was used for extracting total RNA

value: HeLa

value: non-cancer stem cells

tag: transfection

value: ZsGreen-cODCdegron


title: Parental_LAPC-4_cell_line

description: Gene expression of parental cell line

source_name: Parental LAPC-4 cell line


title: LAPC-4_ATRX_KO_clone_1

description: Gene expression after ATRX KO

source_name: LAPC-4 ATRX KO clone 1


title: LAPC-4_ATRX_KO_clone_2

description: Gene expression after ATRX KO

source_name: LAPC-4 ATRX KO clone 2


title: HeLa_CSC, mRNA

source_name: HeLa, CSC

value: cancer stem cells


title: LIFRPos1


title: md1153

first: Heather

last: Rusch

address: 1 Cloister Court, Building 60

department: NINR

institute: NIH

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45°C on HG-U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Partek Genomics Suite software, version 6.6  (GCRMA) using RMA normalization. Analysis of Variance was used to compare differential expression with a fold change cutoff of ±2 with a FDR of ≤.05

label: boitin

source_name: Subject 153, timepoint 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3′ IVT Plus Expression kit, Affymetrix).

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

value: Peripheral blood

tag: case/control

value: PTSD

tag: ptsd subgroup

value: No Follow Up Data

tag: timepoint

value: Baseline

tag: Sex

tag: race

value: Caucasian

tag: ethnicity

value: Not Hispanic


title: md1155

source_name: Subject 155, timepoint 1

tag: tissue

value: Male

tag: age


title: YAP2

value: stem cell-derived beta cells

value: YAP overexpression

value: single cell RNA-seq


title: Control3

value: control


title: YAP3


title: YAP1


title: Control2


title: md1133

source_name: Subject 133, timepoint 1


title: md1145

source_name: Subject 145, timepoint 1

value: Other/Unknown

value: Hispanic


title: md625

source_name: Subject 117, timepoint 2

value: No PTSD

value: Follow-Up


title: md1131

source_name: Subject 131, timepoint 1

value: Black


title: md1130

source_name: Subject 130, timepoint 1


title: md624

source_name: Subject 116, timepoint 2

value: PTSD Improved

value: Mixed Race


title: md1142

source_name: Subject 142, timepoint 1

value: Peripheral blood

value: PTSD


title: Control1


title: md1124

source_name: Subject 124, timepoint 1

value: No Follow Up Data

value: Baseline


title: 20190712 MPRA RNA barcode reads, 4 forskolin, replicate A

city: Los Angeles

first: Jessica

middle: Elizabeth

last: Davis

state: CA

address: 607 Charles E Young Dr E

department: CHEMISTRY AND BIOCHEMISTRY

institute: UCLA

description:
20190712_R4A_BC
total RNA
MPRA barcode reads used for expression analysis

data_processing:
Library strategy: targeted amplicon sequencing
Variant-barcode mapping reads were merged with BBMerge version 9.00. All bbmerge files are presented here following the different libraries. A custom python script was used to map unique barcodes to variants lacking synthesis errors. Briefly, this script searched the last 150 bp of merged reads for sequences perfectly matching the variants designed. The first 20 bp of each merged read was determined to be a barcode and each barcode was then mapped to the most common sequence associated with it, only retaining barcodes that appeared more than twice in merged reads. In order to differentiate between mapped barcodes that are associated with variants with sequencing errors and another variant in the library, we used a Levenshtein distance cut-off of 13 between variants that share a common barcode. This cut-off represented 1% of the total bootstrapped distances between perfect variants in the library. Barcodes mapped to perfect variants were kept if all other variants associated with a barcode fell below this cut-off. This barcode-mapping output is indicated in uniqueSP2345.txt and barcode_statistics_followup.txt and is used in downstream MPRA expression analysis.
MPRA barcode reads were processed using a custom python script to isolate barcode sequences from reads and determine their total number of reads. Briefly, the first 20 sequences were extracted from each read, reverse complemented to match the barcode format from barcode mapping and then the occurence of each of these barcodes was summed as their total number of reads per indexed sample.
Downstream MPRA expression analysis involves only retaining barcodes present in the barcode mapping tables per library. Then barcodes in the DNA sample per each MPRA (indicated by date) are only retained with greater than 6 reads and. Barcode expression is determined by normalizing reads per RNA sample per condition (indicate with the format R#N in which R stands for RNA, # indicates the forskolin concentration and N indicates the replicate). Variants are only analalyzed if they contain at least 8 barcodes in the DNA sample. For 20171129 the nomenclature follows the biological replicate and then the technical replicate (DNA_1_1_BC are barcode reads for the DNA sample, biological replicate 1, technical replicate 1).
Supplementary_files_format_and_content: Barcode mapping tables consisting of barcodes and their associated variants: barcode_statistics_followup.txt; uniqueSP2345.txt

growth_protocol: DMEM with 1% Penicillin-streptomycin and 10% FBS (Thermo Fisher Scientific)

extract_protocol:
Qiagen RNeasy Mini Kits with Qiashredder and on-column DNase I digestions with Qiagen RNase-free DNase Set (Qiagen).
Per sample, RNA was reverse-transcribed using 1.5x the recommended materials for Superscript IV Reverse Transcriptase (Thermo Fisher Scientific. cDNA was amplified with NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs) using input amounts between samples determined from qPCR for a total of 10 cycles. A second PCR was performed in order to add P5 and P7 Illumina flow cell adapter sequences and indices. 0.5 ng was amplified for a total of 7 cycles. Bands were confirmed using Agilent’s D1000 ScreenTape and reagents (Agilent Technologies) on a 2200 Tapestation system.

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 4 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.

tag: cell type

value: H11 BxB1 Landing pad cells


title: 20190712 MPRA DNA barcode reads

description:
20190712_DNA_BC
plasmid
MPRA barcode reads used for expression analysis

growth_protocol: LB

extract_protocol:
QIAprep (Qiagen, Hilden, Germany) spin miniprep kits
Library plasmids mixed at the same ratio as for transfection were used for DNA normalization in the episomal MPRA. 128 ng of this mixture was amplified for 9 cycles. Amplicons were isolated on a 2% TAE gel, after which they were cleaned-up again. A second PCR was performed in order to add P5 and P7 Illumina flow cell adapter sequences and indices. 0.5 ng was amplified for a total of 7 cycles. Bands were confirmed using Agilent’s D1000 ScreenTape and reagents (Agilent Technologies) on a 2200 Tapestation system.

tag: cell line


title: 20190712 MPRA RNA barcode reads, 0 forskolin, replicate A

description:
20190712_R0A_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 0 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: 20170921 MPRA RNA barcode reads, 2^-4 forksolin, replicate B

description:
20170921_R2-4B_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 2^-4 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: 20170921 MPRA RNA barcode reads, 2^-4 forksolin, replicate A

description:
20170921_R2-4A_BC
total RNA
MPRA barcode reads used for expression analysis


title: 20170921 MPRA RNA barcode reads, 2^-3 forksolin, replicate B

description:
20170921_R2-3B_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 2^-3 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: 20170921 MPRA RNA barcode reads, 2^-3 forksolin, replicate A

description:
20170921_R2-3A_BC
total RNA
MPRA barcode reads used for expression analysis


title: md526

source_name: Subject 114, timepoint 2

value: PTSD Not Improved

value: Male

value: Caucasian

value: Not Hispanic


title: 20170921 MPRA RNA barcode reads, 2^-5 forksolin, replicate A

description:
20170921_R2-5A_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 2^-5 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: 20190712 MPRA RNA barcode reads, 4 forskolin, replicate B

description:
20190712_R4B_BC
total RNA
MPRA barcode reads used for expression analysis


title: 20170921 MPRA RNA barcode reads, 2^-5 forksolin, replicate B

description:
20170921_R2-5B_BC
total RNA
MPRA barcode reads used for expression analysis


title: md519

source_name: Subject 107, timepoint 2


title: md523

source_name: Subject 109, timepoint 2

value: Female


title: md516

source_name: Subject 116, timepoint 1


title: md521

source_name: Subject 108, timepoint 2

value: Native Hawaiian/Pacific Islander


title: md515

source_name: Subject 95, timepoint 2

value: Native American


title: md513

source_name: Subject 115, timepoint 1

value: Other/Unknown

value: Hispanic


title: md442

source_name: Subject 109, timepoint 1


title: md441

source_name: Subject 108, timepoint 1

value: No PTSD


title: md454

source_name: subject 112, timepoint 1


title: md383

source_name: Subject 90, timepoint 2

value: PTSD Improved

value: Follow-Up


title: md512

source_name: Subject 114, timepoint 1

value: Peripheral blood


title: md444

source_name: Subject 96, timepoint 2

value: PTSD


title: md514

source_name: Subject 98, timepoint 2

value: Black


title: md518

source_name: Subject 103, timepoint 2


title: md452

source_name: Subject 94, timepoint 2


title: 20170921 MPRA RNA barcode reads, 2^-2 forksolin, replicate B

description:
20170921_R2-2B_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 2^-2 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: 20170921 MPRA RNA barcode reads, 2^2 forksolin, replicate A

description:
20170921_R22A_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 2^2 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: 20170921 MPRA RNA barcode reads, 2^-2 forksolin, replicate A

description:
20170921_R2-2A_BC
total RNA
MPRA barcode reads used for expression analysis


title: 20170921 MPRA RNA barcode reads, 2^-1 forksolin, replicate A

description:
20170921_R2-1A_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 2^-1 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: 20170921 MPRA RNA barcode reads, 2^-1 forksolin, replicate B

description:
20170921_R2-1B_BC
total RNA
MPRA barcode reads used for expression analysis


title: md380

source_name: Subject 107, timepoint 1

value: Baseline

value: Mixed Race


title: md372

source_name: Subject 84, timepoint 2


title: 20170921 MPRA RNA barcode reads, 2^0 forksolin, replicate A

description:
20170921_R20A_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 2^0 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.

value: H11 BxB1 Landing pad cells


title: 20170921 MPRA RNA barcode reads, 2^0 forksolin, replicate B

description:
20170921_R20B_BC
total RNA
MPRA barcode reads used for expression analysis


title: md376

source_name: Subject 87, timepoint 2

value: PTSD Not Improved

value: Male


title: 20170921 MPRA RNA barcode reads, 0 forksolin, replicate A

description:
20170921_R0A_BC
total RNA
MPRA barcode reads used for expression analysis


title: 20170921 MPRA DNA barcode reads

description:
20170921_DNA_BC
plasmid
MPRA barcode reads used for expression analysis


title: 20170921 MPRA RNA barcode reads, 0 forksolin, replicate B

description:
20170921_R0B_BC
total RNA
MPRA barcode reads used for expression analysis


title: 20170631 MPRA RNA barcode reads, 8 forksolin, replicate B

description:
20170631_R8B_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 8 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: md371

source_name: Subject 103, timepoint 1

value: Caucasian

value: Not Hispanic


title: 20170631 MPRA RNA barcode reads, 64 forksolin, replicate A

description:
20170631_R64A_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 64 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: 20170631 MPRA RNA barcode reads, 64 forksolin, replicate B

description:
20170631_R64B_BC
total RNA
MPRA barcode reads used for expression analysis


title: 20170631 MPRA RNA barcode reads, 4 forksolin, replicate A

description:
20170631_R4A_BC
total RNA
MPRA barcode reads used for expression analysis


title: 20170631 MPRA RNA barcode reads, 4 forksolin, replicate B

description:
20170631_R4B_BC
total RNA
MPRA barcode reads used for expression analysis


title: 20170921 MPRA RNA barcode reads, 2^2 forksolin, replicate B

description:
20170921_R22B_BC
total RNA
MPRA barcode reads used for expression analysis


title: 20170631 MPRA RNA barcode reads, 32 forksolin, replicate B

description:
20170631_R32B_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 32 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: 20170631 MPRA RNA barcode reads, 32 forksolin, replicate A

description:
20170631_R32A_BC
total RNA
MPRA barcode reads used for expression analysis


title: 20170631 MPRA RNA barcode reads, 8 forksolin, replicate A

description:
20170631_R8A_BC
total RNA
MPRA barcode reads used for expression analysis


title: md361

source_name: Subject 96, timepoint 1


title: md367

source_name: Subject 80, timepoint 2


title: md318

source_name: Subject 94, timepoint 1


title: md311

source_name: Subject 63, timepoint 2


title: md360

source_name: Subject 76, timepoint 2


title: md365

source_name: Subject 73, timepoint 2


title: md315

source_name: Subject 92, timepoint 1

value: No Follow Up Data


title: md373

source_name: Subject 79, timepoint 2


title: md370

source_name: Subject 102, timepoint 1


title: md307

source_name: Subject 66, timepoint 2


title: 20170631 MPRA RNA barcode reads, 25 forksolin, replicate A

description:
20170631_R25A_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 25 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: 20170631 MPRA RNA barcode reads, 2 forksolin, replicate A

description:
20170631_R2A_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 2 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: 20170631 MPRA RNA barcode reads, 25 forksolin, replicate B

description:
20170631_R25B_BC
total RNA
MPRA barcode reads used for expression analysis


title: 20170631 MPRA RNA barcode reads, 2 forksolin, replicate B

description:
20170631_R2B_BC
total RNA
MPRA barcode reads used for expression analysis


title: md305

source_name: Subject 53, timepoint 2


title: 20170631 MPRA RNA barcode reads, 1 forksolin, replicate B

description:
20170631_R1B_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 1 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: md314

source_name: Subject 72, timepoint 2


title: 20170631 MPRA RNA barcode reads, 1 forksolin, replicate A

description:
20170631_R1A_BC
total RNA
MPRA barcode reads used for expression analysis


title: md308

source_name: Subject 90, timepoint 1


title: md364

source_name: Subject 98, timepoint 1


title: md278

source_name: Subject 57, timepoint 2


title: md310

source_name: Subject 68, timepoint 2


title: md319

source_name: Subject 95, timepoint 1

value: Native American


title: 20170631 MPRA RNA barcode reads, 16 forksolin, replicate B

description:
20170631_R16B_BC
total RNA
MPRA barcode reads used for expression analysis

treatment_protocol: Two mL of a 1.026 x 105 cells/mL stock of H11 Landing Pad cells were plated per 6-well per biological replicate.  The next day, cells were transfected with libraries using Lipofectamine 3000 (Thermo Fisher Scientific). The next day, 2 mL of media with 2x 16 µM forskolin (Sigma Aldrich) was added to the 2 mL media within each 6-well. Cells were stimulated for 3 hours before lysis.


title: 20170631 MPRA RNA barcode reads, 16 forksolin, replicate A

description:
20170631_R16A_BC
total RNA
MPRA barcode reads used for expression analysis


title: 20170631 MPRA RNA barcode reads, 0 forksolin, replicate B

description:
20170631_R0B_BC
total RNA
MPRA barcode reads used for expression analysis


title: 20170631 MPRA RNA barcode reads, 0 forksolin, replicate A

description:
20170631_R0A_BC
total RNA
MPRA barcode reads used for expression analysis


title: md306

source_name: Subject 69, timepoint 2


title: md279

source_name: Subject 56, timepoint 2

value: Female


title: U2OS cells, BLM, BMRP2, PAFAH1B1, PDE6C, PMS2, SPAST, GARS, CHD2 NT DNA rep 1

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

description:
Sample 67
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150

data_processing:
Library strategy: DNA-Seq
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome using BWA-MEM 0.7.9a-r786.
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Files for Indels (Indels.xls) and Base Subtitutions (*variation.txt)

source_name: U2OS cells

growth_protocol: 293FT and U2OS from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) with 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and have been tested for mycoplasma contamination free.

extract_protocol:
For DNA, 72 hr after transfection, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre).
For DNA, DNA-seq libraries were prepared with Illumina TruSeq ChIP Sample Preparation Kit. Deep sequencing was performed on NextSeq 500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: For base editing in genomic DNA, 293FT and U2OS cells were seeded in a 24-well plate at a density of 100 k per well and transfected with 200 μl serum-free Opti-MEM that contained 2.52 μl LIPOFECTAMINE LTX (Life, Invitrogen), 0.84 μl LIPOFECTAMINE plus (Life, Invitrogen), 0.5 μg BE expression vector (BE3, eBE-S3, BE4max, hA3A-eBE-Y130F or dCpf1-eBE expression vector) and 0.34 μg gRNA expression vector.

tag: treatment

value: NT


title: U2OS cells, CDKN2A, DNMT1, DYRK1A, EMX1, FANCF, RUNX1, SITE3, VEGFA NT rep 1

description:
Sample 66
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: U2OS cells, CDKN2A, DNMT1, DYRK1A, EMX1, FANCF, RUNX1, SITE3, VEGFA NT DNA rep 2

description:
Sample 68
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: U2OS cells, BLM, BMRP2, PAFAH1B1, PDE6C, PMS2, SPAST, GARS, CHD2 NT DNA rep 2

description:
Sample 69
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: U2OS cells, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2,  SPAST NT DNA rep 3

description:
Sample 71
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: U2OS cells, FANCF, SITE3, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST dCpf1-eBE DNA rep 3

description:
Sample 65
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: U2OS cells, CDKN2A, DNMT1, DYRK1A, EMX1, FANCF, RUNX1, SITE3, VEGFA NT DNA rep 3

description:
Sample 70
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: md274

source_name: Subject 87, timepoint 1

value: Other/Unknown

value: Hispanic


title: md272

source_name: Subject 85, timepoint 1


title: 20170631 MPRA DNA barcode reads

description:
20170631_DNA_BC
plasmid
MPRA barcode reads used for expression analysis


title: U2OS cells, CDKN2A, DNMT1, EMX1, RUNX1, VEGFA dCpf1-eBE DNA rep 3

description:
Sample 64
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: md253

source_name: Subject 81, timepoint 1

value: No PTSD


title: md271

source_name: Subject 84, timepoint 1

value: Peripheral blood

value: PTSD Improved


title: md264

source_name: Subject 48, timepoint 2

value: PTSD

value: Follow Up


title: U2OS cells, FANCF, SITE3, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST dCpf1-eBE DNA rep 2

description:
Sample 63
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: md250

source_name: Subject 46, timepoint 2


title: md239

source_name: Subject 72, timepoint 1

value: Baseline


title: 20190712 MPRA RNA barcode reads, 0 forskolin, replicate B

description:
20190712_R0B_BC
total RNA
MPRA barcode reads used for expression analysis

value: H11 BxB1 Landing pad cells


title: U2OS cells, CDKN2A, DNMT1, DYRK1A, EMX1, RUNX1, VEGFA dCpf1-eBE DNA rep 2

description:
Sample 62
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: md251

source_name: Subject 79, timepoint 1


title: md517

source_name: Subject 117, timepoint 1


title: md265

source_name: Subject 49, timepoint 2

value: Black


title: md242

source_name: Subject 43, timepoint 2

value: Male

value: Mixed Race


title: md252

source_name: Subject 80, timepoint 1

value: Caucasian

value: Not Hispanic


title: md245

source_name: Subject 76, timepoint 1


title: md237

source_name: Subject 73, timepoint 1


title: md235

source_name: Subject 71, timepoint 1


title: U2OS cells, FANCF,SITE3,BLM,BMRP2,PAFAH1B1,PDE6C,PMS2,SPAST,GARS,CHD2 dCpf1-eBE rep 1 and DYRK1A dCpf1-eBE rep 3

description:
Sample 61
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: md236

source_name: Subject 37, timepoint 2


title: md233

source_name: Subject 69, timepoint 1


title: U2OS cells, CDKN2A, DNMT1, DYRK1A, EMX1, RUNX1, VEGFA dCpf1-eBE DNA rep 1

description:
Sample 60
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150

source_name: U2OS cells


title: md234

source_name: Subject 70, timepoint 1

value: No Follow Up Data


title: U2OS cells, FANCF , SITE3,  BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST hA3A-eBE-Y130F DNA rep 3

description:
Sample 59
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: U2OS cells, CDKN2A, DNMT1, DYRK1A, EMX1, RUNX1, VEGFA hA3A-eBE-Y130F DNA rep 3

description:
Sample 58
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: U2OS cells, FANCF, SITE3, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST hA3A-eBE-Y130F DNA rep 2

description:
Sample 57
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: U2OS cells, CDKN2A, DNMT1, DYRK1A, EMX1, RUNX1, VEGFA hA3A-eBE-Y130F DNA rep 2

description:
Sample 56
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: U2OS cells, CDKN2A, DNMT1, DYRK1A, EMX1, RUNX1, VEGFA hA3A-eBE-Y130F DNA rep 1

description:
Sample 54
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: U2OS cells, CDKN2A, EMX1, FANCF, SITE3, BLM, BMRP2, PAFAH1B1, PDE6C, PMS2, SPAST, GARS, CHD2 eBE-S3 DNA rep 3

description:
Sample 52
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: U2OS cells, DNMT1, DYRK1A, RUNX1, VEGFA eBE-S3 DNA rep 3

description:
Sample 53
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: U2OS cells, FANCF, SITE3, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST hA3A-eBE-Y130F DNA rep 1

description:
Sample 55
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: U2OS cells, DNMT1, DYRK1A, RUNX1, VEGFA eBE-S3 DNA rep 2

description:
Sample 51
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: U2OS cells, DNMT1, DYRK1A, RUNX1, VEGFA eBE-S3 DNA rep 1

description:
Sample 49
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: U2OS cells, CDKN2A, EMX1, FANCF, SITE3, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST eBE-S3 DNA rep 1

description:
Sample 48
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: U2OS cells, CDKN2A, EMX1, FANCF, SITE3, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST eBE-S3 DNA rep 2

description:
Sample 50
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: 293FT cells, BLM, BMRP2, CHD2, PAFAH1B1, PDE6C, PMS2, SPAST, GARS NT DNA rep 3

description:
Sample 47
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150

source_name: 293FT cells


title: 293FT cells, CDKN2A, DNMT1, DYRK1A, EMX1, FANCF, RUNX1, SITE3, VEGFA NT DNA rep 3

description:
Sample 46
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST NT DNA rep 2

description:
Sample 45
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: 293FT cells, CDKN2A, DNMT1, DYRK1A, EMX1, FANCF, RUNX1, SITE3, VEGFA NT DNA rep 2

description:
Sample 44
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: md186

source_name: Subject 38, timepoint 2


title: md190

source_name: Subject 66, timepoint 1


title: 293FT cells, CDKN2A, DNMT1, DYRK1A, EMX1, FANCF, RUNX1, SITE3, VEGFA NT rep 1

description:
Sample 42
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, BLM, BMRP2, CHD2, GARS,PAFAH1B1, PDE6C, PMS2, SPAST NT DNA rep 1

description:
Sample 43
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: md188

source_name: Subject 64, timepoint 1


title: md157

source_name: Subject 24, timepoint 2

value: PTSD Not Improved


title: 293FT cells, CDKN2A, DYRK1A, RUNX1, VEGFA dCpf1-eBE DNA rep 3

description:
Sample 40
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, DNMT1, EMX1, FANCF, SITE3, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST dCpf1-eBE DNA rep 3

description:
Sample 41
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: md192

source_name: Subject 68, timepoint 1


title: md181

source_name: Subject 34, timepoint 2


title: md177

source_name: Subject 57, timepoint 1


title: md168

source_name: Subject 53, timepoint 1


title: md164

source_name: Subject 46, timepoint 1


title: md160

source_name: Subject 48, timepoint 1


title: 293FT cells, DNMT1, EMX1, FANCF, SITE3, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST dCpf1-eBE DNA rep 2

description:
Sample 39
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: md171

source_name: Subject 32, timepoint 2


title: md176

source_name: Subject 56, timepoint 1

value: Female


title: md187

source_name: Subject 63, timepoint 1

value: Other/Unknown


title: md166

source_name: Subject 36, timepoint 2


title: md165

source_name: Subject 50, timepoint 1


title: 293FT cells, CDKN2A, DYRK1A, RUNX1, VEGFA dCpf1-eBE DNA rep 2

description:
Sample 38
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: md159

source_name: Subject 18, timepoint 2


title: md184

source_name: Subject 61, timepoint 1


title: 293FT cells, DYRK1A, FANCF, SITE3, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST hA3A-eBE-Y130F DNA rep 3

description:
Sample 35
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150

source_name: 293FT cells


title: 293FT cells, DNMT1, EMX1, FANCF, SITE3, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST dCpf1-eBE DNA rep 1

description:
Sample 37
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: 293FT cells, CDKN2A, DYRK1A, RUNX1, VEGFA dCpf1-eBE DNA rep 1

description:
Sample 36
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, CDKN2A, DNMT1, EMX1, RUNX1, VEGFA hA3A-eBE-Y130F DNA rep 3

description:
Sample 34
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, DYRK1A, FANCF, SITE3, BLM, BMRP2, PAFAH1B1, PDE6C, PMS2, SPAST, GARS, CHD2 hA3A-eBE-Y130F DNA rep 1

description:
Sample 31
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: 293FT cells, DYRK1A, FANCF, SITE3, BLM, BMRP2, PAFAH1B1, PDE6C, PMS2, SPAST, GARS, CHD2 hA3A-eBE-Y130F DNA rep 2

description:
Sample 33
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: 293FT cells, DYRK1A, FANCF, SITE3, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST eBE-S3 DNA rep 3

description:
Sample 29
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: md139

source_name: Subject 38, timepoint 1


title: md156

source_name: Subject 14, timepoint 2


title: md163

source_name: Subject 49, timepoint 1


title: 293FT cells, CDKN2A, DNMT1, EMX1, RUNX1, VEGFA eBE-S3 DNA rep 3

description:
Sample 28
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: md149

source_name: Subject 43, timepoint 1


title: md141

source_name: Subject 9, timepoint 2


title: md140

source_name: Subject 7, timepoint 2

value: Asian


title: md152

source_name: Subject 10, timepoint 2

value: No PTSD


title: 293FT cells, CDKN2A, DNMT1, EMX1, RUNX1, VEGFA hA3A-eBE-Y130 DNA rep 2

description:
Sample 32
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, DYRK1A, FANCF, SITE3, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST, eBE-S3 DNA rep 2

description:
Sample 27
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: 293FT cells, CDKN2A, DNMT1, EMX1, RUNX1, VEGFA hA3A-eBE-Y130F DNA rep 1

description:
Sample 30
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, CDKN2A, DNMT1, EMX1, RUNX1, VEGFA eBE-S3 DNA rep 1

description:
Sample 24
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: md129

source_name: Subject 3, timepoint 2

value: Peripheral blood


title: md137

source_name: Subject 32, Timepoint 1


title: 293FT cells, DNMT1, DYRK1A, VEGFA, BMRP2, PAFH1B1, SPAST, BTK, CLN6, PGM3 NT DNA rep 2

description:
Sample 22
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150

value: NT


title: 293FT cells, DNMT1, DYRK1A, VEGFA, BMRP2, PAFH1B1, SPAST, BTK, CLN6, PGM3 NT DNA rep 3

description:
Sample 23
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: md135

source_name: Subject 34, timepoint 1

value: PTSD

value: PTSD Improved


title: 293FT cells, DYRK1A, FANCF, SITE3, BLM, BMRP2, CHD2, GARS, PAFAH1B1, PDE6C, PMS2, SPAST eBE-S3 DNA rep 1

description:
Sample 25
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 100-150


title: md113

source_name: Subject 16, timepoint 1

value: Baseline


title: md138

source_name: Subject 37, timepoint 1


title: 293FT cells, DNMT1, VEGFA, BTK, CLN6, PGM3 dCpf1-eBE DNA rep 2

description:
Sample 19
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: md122

source_name: Subject 25, timepoint 1


title: md136

source_name: Subject 36, timepoint 1


title: md121

source_name: Subject 23, timepoint 1


title: md117

source_name: Subject 21, timepoint 1

value: Native Hawaiian/Pacific Islander


title: md123

source_name: Subject 1, timepoint 2

value: Follow Up

value: Black

value: Hispanic


title: md114

source_name: Subject 18, timepoint 1

value: Male

value: Caucasian


title: md112

source_name: Subject 10, timepoint 1

value: Not Hispanic


title: md109

source_name: Subject 9, timepoint 1


title: md104

source_name: Subject 14, timepoint 1


title: 293FT cells, DYRK1A, VEGFA, BMRP2, PAFH1B1, SPAST, BTK, CLN6 dCpf1-eBE DNA rep 1

description:
Sample 18
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150

source_name: 293FT cells


title: 293FT cells, DNMT1, DYRK1A, VEGFA, BMRP2, PAFH1B1, SPAST, BTK, CLN6, PGM3 NT DNA rep 1

description:
Sample 21
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, DNMT1, DYRK1A, VEGFA, BMRP2, PAFH1B1, SPAST, BTK, CLN6, PGM3 dCpf1-eBE DNA rep 3

description:
Sample 20
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, DNMT1 hA3A-eBE-Y130F DNA rep 1 and DYRK1A, BMRP2, PAFH1B1, SPAST, BTK, CLN6, PGM3 hA3A-eBE-Y130F DNA rep 2

description:
Sample 14
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, DNMT1, VEGFA hA3A-eBE-Y130F DNA rep 2 and CLN6, PGM3 hA3A-eBE-Y130F DNA rep 3

description:
Sample 15
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, DYRK1A, VEGFA, BMRP2, PAFH1B1, SPAST, BTK, CLN6, PGM3 hA3A-eBE-Y130F DNA rep1

description:
Sample 13
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, VEGFA BE4max DNA rep 2 and SPAST BE4max DNA rep 3

description:
Sample 11
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, DNMT1, PGM3 dCpf1-eBE DNA rep 1 and DYRK1A, BMRP2, PAFH1B1, SPAST dCpf1-eBE DNA rep 2

description:
Sample 17
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, DNMT1, DYRK1A, BMRP2, PAFH1B1, SPAST, BTK, CLN6, PGM3 BE4max DNA rep 2

description:
Sample 10
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: md103

source_name: Subject 3, timepoint 1


title: md101

source_name: Subject 1, timepoint 1


title: 293FT cells, DNMT1, DYRK1A, VEGFA, BMRP2, PAFH1B1, SPAST, BTK hA3A-eBE-Y130F DNA rep 3

description:
Sample 16
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: md102

source_name: Subject 2, timepoint 1


title: 293FT cells, CDKN2A, DNMT1, EMX1, RUNX1, VEGFA eBE-S3 DNA rep 2

description:
Sample 26
Indels_sample24-71.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, DNMT1, VEGFA, SPAST eBE-S3 DNA rep 2 and BTK, CLN6 eBE-S3 DNA rep 3

description:
Sample 7
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, DNMT1, DYRK1A, VEGFA, BMRP2, PAFH1B1, SPAST, BTK, CLN6, PGM3 BE4max DNA rep 1

description:
Sample 9
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: md107

source_name: Subject 7, timepoint 1

value: PTSD Not Improved


title: 293FT cells, DNMT1, DYRK1A, VEGFA, BMRP2, PAFH1B1, BTK, CLN6, PGM3 BE4max DNA rep 3

description:
Sample 12
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 254706910158_b4 - col0_flg22_rep3 vs col0_rep3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Is the dgk5.1 mutant impaired in its response to flagellin?

hyb_protocol: col0_rep3 Cy5 / col0_flg22_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: seedling - Media: Murashige-Skoog liquid media supplemented with vitamins. Temperature: 22°C Light: 16h light / 8h dark

extract_protocol: col0_rep3:200mg. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: columbia

tag: genotype

value: wildtype

value: 15.9day dev.stage (Boyes et al. Plant Cell 2001):boyes:1.03

treatment_protocol: Name:Flagellin treatment - compound based treatment - compound addition,flg22:quantity 1uM time 1hour . 2-weeks old Arabidopsis thaliana entire seedlings (stage 1.04) of Col-0 or dgk5.1, cultivated in MS liquid media, 22°C, 16h/8h light cycle were treated by adding flg22 up to final concentration 1µM. After 1h samples were fixed and total RNA was extracted using RNeasy Mini Kit (Qiagen).


title: 254706910158_b3 - col0_rep3 vs col0_flg22_rep3

hyb_protocol: col0_flg22_rep3 Cy5 / col0_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910158_b2 - dgk5.1_flg22_rep3 vs dgk5.1_rep3

hyb_protocol: dgk5.1_rep3 Cy5 / dgk5.1_flg22_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: dgk5.1_rep3:200mg. (Qiagen_RNeasy.pdf)

value: dgk5 mutant


title: 254706910158_b1 - dgk5.1_rep3 vs dgk5.1_flg22_rep3

hyb_protocol: dgk5.1_flg22_rep3 Cy5 / dgk5.1_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910153_b4 - dgk5.1_flg22_rep2 vs dgk5.1_rep2

hyb_protocol: dgk5.1_rep2 Cy5 / dgk5.1_flg22_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: dgk5.1_rep2:200mg. (Qiagen_RNeasy.pdf)


title: 254706910152_b4 - col0_flg22_rep2 vs col0_rep2

hyb_protocol: col0_rep2 Cy5 / col0_flg22_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: col0_rep2:200mg. (Qiagen_RNeasy.pdf)


title: 254706910153_b2 - dgk5.1_flg22_rep1 vs dgk5.1_rep1

hyb_protocol: dgk5.1_rep1 Cy5 / dgk5.1_flg22_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: dgk5.1_rep1:200mg. (Qiagen_RNeasy.pdf)


title: 254706910153_b1 - dgk5.1_rep1 vs dgk5.1_flg22_rep1

hyb_protocol: dgk5.1_flg22_rep1 Cy5 / dgk5.1_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910157_b1 - col0_rep3 vs dgk5.1_rep3

hyb_protocol: dgk5.1_rep3 Cy5 / col0_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910153_b3 - dgk5.1_rep2 vs dgk5.1_flg22_rep2

hyb_protocol: dgk5.1_flg22_rep2 Cy5 / dgk5.1_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 293FT cells, DNMT1, SPAST  eBE-S3 DNA rep 1 and DYRK1A, BMRP2, PAFH1B1, BTK, CLN6, PGM3 eBE-S3 DNA rep 2

description:
Sample 5
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 293FT cells, DNMT1, DYRK1A, VEGFA, BMRP2, PAFH1B1, SPAST, BTK, PGM3 BE3 DNA rep 3

description:
Sample 4
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 254706910152_b3 - col0_rep2 vs col0_flg22_rep2

hyb_protocol: col0_flg22_rep2 Cy5 / col0_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Ume6_E-ChRP_13hr_RAF_RNA-seq_rep2

city: Eugene

first: Jeffrey

middle: N

last: McKnight

state: OR

address: 1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2
Strands were separated into Watson and Crick strands using SAMtools filtering
Read counts were piled up across the yeast genome
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: tab-delimited chromosome/position/RNA read counts; coverage file (chr, position, count)

organism: Saccharomyces cerevisiae

source_name: exponentially-growing W303 yeast cells

growth_protocol: grown to mid-log

extract_protocol:
RNA was extracted using hot-acid phenol ; rRNA was depleted using Illumina Ribo-Zero Gold (Yeast)
cDNA libraries were constructed with the NuGEN Universal mRNA Library Kit as per instructions

tag: strain background

value: W303 ume6

tag: e-chrp added

tag: spytagged-factor

tag: expression promoter

value: GAL (integrated at HO locus)

value: 2% raffinose added for 13hr


title: 293FT cells, DYRK1A, VEGFA, BMRP2, PAFH1B1, BTK, CLN6, PGM3 eBE-S3 DNA rep 1

description:
Sample 6
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: Control input

description:
Control siRNA treated CD8+ T cell
Control siRNA specific peaks.txt

source_name: CD8+ T cells

extract_protocol: H3K27ac was purified with anti-H3K27ac antibody and RNA was extracted from cells using TRIZOL reagent.

tag: harvest time

value: Cells from Homo sapiens

value: Control siRNA transfection


title: Ume6_E-ChRP_13hr_RAF_RNA-seq_rep1


title: Ume6_E-ChRP_13hr_GAL_RNA-seq_rep2

value: W303 WT

value: 2% galactose added for 13hr


title: 293FT cells, VEGFA, BMRP2, SPAST BE3 DNA rep 1 and DNMT1, DYRK1A , PAFH1B1, CLN6, PGM3 BE3 DNA rep 2

description:
Sample 2
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: 254706910157_b2 - dgk5.1_rep3 vs col0_rep3

hyb_protocol: col0_rep3 Cy5 / dgk5.1_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 293FT cells, DNMT1, DYRK1A, PAFH1B1, BTK, CLN6, PGM3 BE3 DNA rep 1

description:
Sample 1
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: Ume6_E-ChRP_13hr_GAL_RNA-seq_rep1


title: 293FT cells, DNMT1, DYRK1A, VEGFA, BMRP2, PAFH1B1, SPAST, PGM3 eBE-S3 DNA rep 3

description:
Sample 8
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: Spycatcher_E-ChRP_Reb1-Spytag_13hrs_RAF_RNA_rep2


title: Spycatcher_E-ChRP_Reb1-Spytag_13hrs_RAF_RNA_rep1


title: 293FT cells, VEGFA, BMRP2, SPAST, BTK BE3 DNA rep 2 and CLN6 BE3 DNA rep 3

description:
Sample 3
Indels_sample1-23.xls
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 105-150


title: Spycatcher_E-ChRP_Reb1-Spytag_13hrs_GAL_RNA_rep2


title: OCI-Ly1-CONTROL-sg2-01 [ATAC-seq]

first: Candace

last: Patterson

address: 75 Ames St

institute: The Broad Institute

description:
NTg2_1
20170702_NTg2_ATAC_Ad2_4_7_CO4516_S4

data_processing:
Samples were sequenced on an Illumina NextSeq 500, 35 base pair cycles in paired-end mode. ATAC-seq reads in fastq format were trimmed to remove adapter sequences using skewer v0.2.2.
Trimmed reads were aligned to hg19 using bowtie2 v2.3.3.1 (Langmead and Salzberg, 2012)
Alignments were filtered using samtools v1.9 (Li and Durbin, 2009) to remove duplicate reads and retain only proper pairs with mapping quality greater than 30
Reads mapping to blacklisted regions were removed using samtools v1.9.
Reads were converted to bed format and reads on the forward and reverse strands were shifted +4 and -5 bp respectively.
MACS2 v2.1.1 (Zhang et al., 2008) was used to call peaks
IDR v2.0.4.2 was used to filter enriched regions at an IDR of less than 0.05 to produce high-confidence peak and summit sets. High-confidence summits were expanded to 500bp and a count matrix was generated with Rsubread v1.30.9 (Chen et al., 2016).
This matrix was imported to R and chromVAR (Schep et al., 2017) was used in conjunction with motifs in the JASPAR2018 (10.18129/B9.bioc.JASPAR2018) (Khan et al., 2018) and chromVARmotifs (https://github.com/GreenleafLab/chromVARmotifs) R packages to generate motif-level measures of differential accessibility.
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated values (differential accessibility z−score); bigwig containing 10bp binned Tn5 insertion counts normalized to millions of reads in peaks.

extract_protocol:
ATAC-seq was performed on 50,000 cells as described (Buenrostro et al., 2013).
Transposition reactions were performed for 1 hr at 37° C, followed by purification and sample barcoding by PCR.

tag: genotype/variation

value: CONTROL (non targeting sgRNAs)


title: OCI-Ly1-CONTROL-sg2-02 [ATAC-seq]

description:
NTg2_2
20170705_NTg2_ATAC_Ad2_4_7_CO4516-2_S4


title: OCI-Ly1-CONTROL-sg1-02 [ATAC-seq]

description:
NTg1_2
20170705_NTg1_ATAC_Ad2_3_5_CO4516-2_S3


title: Spycatcher_E-ChRP_Reb1-Spytag_13hrs_GAL_RNA_rep1


title: OCI-Ly1-parental-02 [ATAC-seq]

description:
Ly1_2
20170705_Ly1_ATAC_Ad2_1_1_CO4516-2_S1


title: OCI-Ly1-CONTROL-sg1-01 [ATAC-seq]

description:
NTg1_1
20170702_NTg1_ATAC_Ad2_3_5_CO4516_S3


title: ume6DELTA_dCas9_E-ChRP_noTarget-1_MNase

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2
Dyads were calculated by taking the midpoint of paired-end reads from fragments between 100 and 200 bp
Data were normalized such that average value at a genomic position was 1.0
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: tab-delimited chromosome/position/normalized dyad counts; coverage file (chr, position, count)

growth_protocol:
exponentially-growing W303 yeast cells
grown to mid-log

extract_protocol:
cells were crosslinked with 1% formaldehyde for 20 min, spheroplasted, digested with micrococcal nuclease, crosslinks reversed overnight at 65 degrees with proteinase K treatment, phenol-chloroform extracted, RNase-treated, mononucleosome band gel-extracted and CIP-treated
CIP-treated nucleosome-sized DNA footprints were converted to libraries with NuGEN Ovation Ultralow kit

value: ADH1 (on pRS416)

tag: molecule subtype

value: Nucleosomal DNA

value: no gRNA


title: 254706910152_b2 - col0_flg22_rep1 vs col0_rep1

hyb_protocol: col0_rep1 Cy5 / col0_flg22_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: col0_rep1:200mg. (Qiagen_RNeasy.pdf)


title: OCI-Ly1-ID3-sg2-02 [ATAC-seq]

description:
ID3g2_2
20170705_ID3g2_ATAC_Ad2_12_23_CO4516-2_S12

value: ID3 knocked-out


title: 254706910151_b2 - dgk5.1_rep1 vs col0_rep1

hyb_protocol: col0_rep1 Cy5 / dgk5.1_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910152_b1 - col0_rep1 vs col0_flg22_rep1

hyb_protocol: col0_flg22_rep1 Cy5 / col0_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.