title: TER119-SIINFEKL_3

city: Chicago

first: Jeffrey

middle: Alan

last: Hubbell

address: 5640 South Ellis Avenue, ERC 369

department: Institute for Molecular Engineering

institute: University of Chicago

description:
PolyA RNA
tsin.2
Processed data file: Normalized_Reads_count_RPKM.txt

data_processing:
Demultiplexing was done using Illumina “bcl2fastq2-v2.17.1.14” software.
Single end reads were aligned to the mouse genome (assembly GRCm38/mm10) using STAR 2.4.2.a with default parameters. A genome index was built using Ensembl annotation.
For each Ensembl gene, all of the exons of the respective annotated protein-coding transcripts were considered. Reads up to one mismatch were counted, considering only reads in the right gene orientation. Genes were not considered for analysis if the average number of read was lower than 100 reads in more than two conditions, or in the case of genes with less than 10 reads in a certain condition. Read counts were normalized by the respective library size using EdgeR, and by the average size of transcripts (RPKM). Log2 gene expression levels were calculated and reported.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Normalized_Reads_count_RPKM.txt: Tab-delimited text file includes RPMK (log2) values for each sample.

source_name: ovalbumin-specific CD8+ T cells isolated from spleen of OTI mice

growth_protocol: CD8+ T cells from the spleen of OTI mice were isolated using a CD8+ magnetic bead negative selection kit (Miltenyi Biotec), following the manufacturer’s instructions. On day 0, 10e6 CFSE-labeled CD8+ OTI cells were injected i.v. in 100 μL of PBS into the tail vein of recipient CD45.2+ C57BL/6 mice.

extract_protocol:
Mice were euthanized on day 4 and spleens were harvested for OTI CD8+ T cell isolation. Splenocytes were exposed for 5 min at RT to 0.155 M NH4Cl to lyse erythrocytes. A first round of isolation was performed for CD8+ T cell isolation using a CD8+ magnetic bead negative selection kit (Miltenyi Biotec), following the manufacturer’s instructions. The following staining steps were performed on ice. Cells were washed with PBS and stained for 15 min in PBS + 2% FBS with CD3e FITC, CD45.1 PE-Cy7, CD8 APC-e780, and CD4 Pacific blue antibodies (eBioscience). Cells were resuspended at a concentration of 8x10e6 cells/mL in PBS + 1 mM EDTA, and OTI CD8+ T cells were sorted using a FACS ARIAII cytometer. Viable transgenic OTI CD8+ T cells were gated based on their expression of the CD3e, CD8 and CD45.1 markers. Total RNA was extracted from sorted OTI CD8+ T cells using a RNeasy Plus Micro kit (Qiagen), following the manufacturer’s instructions.
Libraries were generated using an Illumina RNA-SEQ kit (TruSeq® Stranded mRNA LT -- SetA, RS-122-2101).

treatment_protocol: One day following adoptive transfer, 223 pmol (equivalent to 10 μg of OVA) of ERY1-OVA, TER119-SIINFEKL, OVA or SIINFEKL peptide were injected i.v. in a 100 μL volume of saline.

tag: strain/background

value: OTI

tag: recipient strain/background

value: 8-12 weeks

value: CD8+ T cells

value: erythrocyte-targeted SIINFEKL MHCI peptide


title: Naive_3

status: Public on May 05 2020

type: SRA

state: IL

country: USA

description:
PolyA RNA
cont.2
Processed data file: Normalized_Reads_count_RPKM.txt

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: age

tag: cell type

tag: treatment

value: saline


title: TER119-SIINFEKL_1

description:
PolyA RNA
tsin
Processed data file: Normalized_Reads_count_RPKM.txt


title: ips_18_ATAC_Seq

city: Evanston

first: Jubao

last: Duan

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

library_source: genomic

data_processing:
ATAC-Seq data: All raw sequence reads generated by Illumina HiSeq 2000 have been de-complexed at the University of Minnesota Genomic Center and provided as 2x50 bp pair-end fastq files (100 M reads per sample). Adapter remnants, low-quality reads, and low QSEQ short sequences near either end of reads were processed by Trimmomatic (ILLUMINACLIP:NexteraPE-PE.fa:2:30:7, SLIDINGWINDOW:3:18, MINLENGTH:26). The survived sequences were separated into pair-end and single-end fastq files per sample, respectively. The pair-end and single-end fastq files were individually mapped against the human genome reference file including decoy sequences (GRCh38p7/hg38, 1000 Genome Project) using bowtie2 (-x 2000, -mm --qc-filter –met 1 –sensitive –no-mixed -t) and subsequently merged and sorted as BAM-formatted files using samtools, only uniquely mapped reads (MAPQ > 30) were collected. Picard tools MarkDuplicate was then used to remove all PCR and optical duplicated reads from the BAM file.
RNA-Seq data: RNA sequencing files were provided in the format of 2x150 bp pair-end (25 M reads per sample) fastq files. Briefly, libraries were prepared using the NEB Nextera kit with customised adapters. Since the sequencing facility had performed pre-cleaning on raw reads, no Trimmomatic action was performed. The files were subsequently mapped to the human hg38 genome (GRCh38p7) using STAR v 2.6.0 (--outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outSAMattrIHstart 0 --outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterIntronMotifs RemoveNoncanonical --outBAMcompression 10 --outBAMsortingThreadN 20 --outBAMsortingBinsN 20 --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --outSJfilterReads Unique --limitBAMsortRAM 10000000000 --alignSoftClipAtReferenceEnds No --quantTranscriptomeBAMcompression 10 10 ).
Genome_build: GRCh38.p7

molecule: genomic DNA

organism: Homo sapiens

source_name: iPS Cell

extract_protocol:
For ATAC-seq, we harvested 50,000 cells by centrifugation at 500 g x 5 min at 4C. We washed cells once with PBS buffer and resuspended the cell pellets in 50 uL of cold lysis buffer (10 mM Tris-HCl, pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA- 630). We collected cell pellets, discarded the supernatants, and immediately continued to transposition reaction in 50 uL transposition reaction mix. We incubated the transposition reaction at 37C for 30 min, immediately followed by purification through a QIAGEN MinElute Kit. We stored the purified DNAs at  20 C until generating sequencing library.
The library was generated and sequenced at University of Minnesota Genomic Center.We have followed the protocol as previously described (Buenrostro et al., 2013) with minor modifications. Specifically, we thawed the transposed and purified DNAs and carried out PCR in 50 uL of reaction with NEBNext High Fidelity 2X Master mix and 5 ul of 25 mM Forward/Reverse ATAC-seq index, i.e., standard barcoded primers of Nextera kit (FC-121-1030), for each sample. After reaction, we purified samples with SPRI beads and eluted the PCR products in 12 uL elution buffer. We checked the DNA library by picogreen quantification and the size of the fragments with an Agilent High Sensitivity DNA chip. Libraries were diluted to 2 nM and pooled for downstream sequencing.
The library was generated and sequenced at University of Minnesota Genomic Center.We have followed the protocol as previously described (Buenrostro et al., 2013) with minor modifications: (1) using the standard Nextera primer set for PCR amplification of the transposed DNA fragments, (2) monitoring qPCR reaction to determine the number of additional cycles for full PCR amplification, and (3) using Agilent High Sensitivity DNA chip for library size validation. Specifically, we thawed the transposed and purified DNAs and carried out an initial 5-cycle PCR (1 cycle: 72 C for 5 min; 1 cycle: 98 C for 30 s; then 5 cycles: 98 C for 10 s, 63 C for 30 s, 72 C for 1 min) in a 50 mL of reaction including NEBNext High Fidelity 2X Master mix and 5 mL of 25 mMForward/Reverse ATAC-seq index, i.e., standard barcoded primers of Nextera kit (FC-121-1030), for each sample.We then used qPCR to determine the number of additional cycles of PCR amplification that were required, by using the cycle number that corresponds to 1/3 of the maximum fluorescent intensity (typically +5, +6, +7) shown on real-time PCR plots on ABI7900 (Applied Biosystems). After the reactions were subjected to additional PCR cycles, we purified each sample with SPRI beads and eluted the PCR products in 12 mL elution buffer. We checked the DNA library by picogreen quantification and the size of the fragments with an Agilent High Sensitivity DNA chip (the library should be sized between 200-700 bp). Libraries were diluted to 2 nM and pooled for downstream sequencing. For the initial OCR profiling, we pooled all the 6 libraries (2 for iPSC, 1 for N-d27, 1 for N-d33, and 2 for N-d41) and sequenced on a HiSeq 2500 using a PE 2x50 bp flow cell in a single sequencing lane. For the additional ATAC-seq on the unedited and edited iNs, we followed the same procedures as described above. We achieved > 120 million passing-filter reads for the lane and the average quality scores for all libraries are all above Q30 for both R1 and R2.

treatment_protocol: hiPSCs were cultured using feeder-free method on geltrex (Thermofisher)-coated plate in mTeSR1 media (StemCell). Media were changed daily and cells were passaged as single cells every 4-6 days using accutase (Thermofisher) in mTeSR1 in the presence of 5 mM ROCK inhibitor (R&D Systems)

value: iPS lines used to differentiate into all cell types


title: NSC_04_ATAC_Seq

source_name: Neural Progenitor Cell

treatment_protocol: NPC are prepared using PSC Neural Induction Medium (Thermofisher) following vendor’s protocol with modification. Briefly, hiPSCs were replated as clumps in mTeSR media (STEMCELL) supplemented with 5 µM ROCK inhibitor (R&D Systems) on Day 0. From Day 1 to Day 9, cells were treated in PSC Neural Induction Medium with routinely removal of differentiated non-neuron cells. PSC Neural Induction Medium was prepared as 490ml Neurobasal Medium (Thermofisher) and 10 ml Neural Induction Supplement (Thermofisher). On Day 10, P0 NPCs were ready for passaging. From P0 to P3, NPCs were passaged using Rosette Selection Reagent (STEMCELL) and expanded in Neural Expansion Medium. Neural Expansion Medium was prepared as 245 ml Neurobasal Medium, 245 ml Advanced DMEM⁄F-12 media (Thermofisher) and 10ml Neural Induction Supplement. From P4, NPCs were passaged as single cells using Accutase (Thermofisher). 5 µM ROCK inhibitor were supplemented into media on the day of passage and withdrawn 24 hr post replating.

value: iPS-derived Neural Progenitor Cell


title: NSC_03_ATAC_Seq


title: ips_16_ATAC_Seq


title: ips_21_ATAC_Seq


title: ips_12_ATAC_Seq


title: NSC_02_ATAC_Seq


title: TER119-SIINFEKL_2

description:
PolyA RNA
tsin.1
Processed data file: Normalized_Reads_count_RPKM.txt


title: OVA_1

description:
PolyA RNA
ova
Processed data file: Normalized_Reads_count_RPKM.txt

value: ovalbumin


title: GA-07_S21_ATAC_Seq

source_name: GABergic , day-28 post induction

treatment_protocol: To prepare GABAergic neurons, NPCs were single-cell seeded in Virus-Neural Expansion Medium Cocktail onto laminin-coated (Sigma) plate at 200,000 cells per cm2 on Day 0. Virus-Neural Expansion Medium Cocktail was prepared as 7 ml Neural Expansion Media, 1 ml rtTA virus, 1 ml Ascl1-puro virus, 1 ml Dlx2-hygro virus and 5 µM ROCK inhibitor. On day 1, virus  were withdrawn and cells were fed with fresh Neural Expansion Media supplemented with 2µg/ml doxycycline (Sigma). From Day 2 to Day 6, cells were treated in Neural Expansion Media supplemented with 2 µg/ml doxycycline, 2 µg/ml puromycin (Thermofisher) and 100 µg/ml hygromycin (Thermofisher) to remove non-transduced cells. On day 7, switched media to conditioned NeuralbasalPlus Media and change media every 3 days. NeuralbasalPlus Media was conditioned using rat astrocyte (Thermofisher) 24 hr before media changing and BDNF, GDNF, NT-3. Doxycycline was withdrawn on Day 16 and 50 nM Ara-C was included in media if non-neuron cells were observed. On Day 28, neurons were harvested using Accutase for ATAC-seq or RNA isolation.

value: iPS-derived GABAergic Neurons, 28 days post induction


title: ERY1-OVA_1

description:
PolyA RNA
eryova
Processed data file: Normalized_Reads_count_RPKM.txt

value: erythrocyte-targeted ovalbumin


title: OVA_3

description:
PolyA RNA
ova.2
Processed data file: Normalized_Reads_count_RPKM.txt


title: Naive_1

description:
PolyA RNA
cont
Processed data file: Normalized_Reads_count_RPKM.txt


title: ERY1-OVA_3

description:
PolyA RNA
eryova.2
Processed data file: Normalized_Reads_count_RPKM.txt


title: ERY1-OVA_2

description:
PolyA RNA
eryova.1
Processed data file: Normalized_Reads_count_RPKM.txt


title: GA-05_S20_ATAC_Seq


title: Naive_2

description:
PolyA RNA
cont.1
Processed data file: Normalized_Reads_count_RPKM.txt


title: SIINFEKL_2

description:
PolyA RNA
sin.1
Processed data file: Normalized_Reads_count_RPKM.txt

value: SIINFEKL MHCI peptide


title: GA-04_S19_ATAC_Seq


title: GA-11_S24_ATAC_Seq


title: ips_08_ATAC_Seq


title: GA-18_S26_ATAC_Seq


title: ips_11_ATAC_Seq


title: GA-12_S25_ATAC_Seq


title: ips_09_ATAC_Seq


title: SIINFEKL_1

description:
PolyA RNA
sin
Processed data file: Normalized_Reads_count_RPKM.txt


title: OVA_2

description:
PolyA RNA
ova.1
Processed data file: Normalized_Reads_count_RPKM.txt


title: GA-09_S23_ATAC_Seq


title: DN_21_ATAC_Seq

source_name: Dopaminergic, day-30 post induction


title: DN_16_ATAC_Seq

treatment_protocol: The protocol for differentiation of dopaminergic neurons was adapted from Gonzalez et al. Briefly, NPCs were single-cell seeded in Neural Expansion Medium onto 6 well plate coated with Geltrex (Thermofisher). Dopaminergic priming media was added to the cells at 50% confluency on Day 0. Dopaminergic priming media was prepared by adding Neurobasal medium (Thermofisher) with the following components: N2 supplement (Thermofisher), B27 supplement (Thermofisher), 100 µg/ml Primocin (Invivogen), Glutamax (Thermofisher), 2 µM purmorphamine (Tocris), 100 ng/ml FGF8 (Thermofisher) and 0.25 µM SAG (R&D). Purmorphamine, FGF8 and SAG were added upon use. Media was changed on Day 2, 4 and 6. On Day 7 the cells were replated onto 6 well plate coated with Geltrex at 5x105 cells/well and media was switched to Dopaminergic differentiation media. Dopaminergic differentiation media was prepared by adding to Neurobasal medium the following components: B27 supplement, 100 µg/ml Primocin, Glutamax, 0.2 mM ascorbic acid (Sigma), 10 ng/µl BDNG (PeproTech), 10 ng/µl GDNF (PeproTech), 1 ng/µl TGFβ3 (PeproTech) and 0.1 mM cAMP (EMD). On Day 30 dopaminergic neurons were harvested using Accutase (Thermofisher) for ATAC-seq and RNA isolation.

value: iPS-derived Dopaminergic Neurons, 30 days post induction


title: d5A2n

city: Saitama

first: Peixun

last: Han

address: Hirosawa Wako

country: Japan

institute: Riken

description:
Ribosome Profiling
processed data file: d5An.merge.1.txt

data_processing:
Library strategy: Ribo-seq
Basecalling with Illumina Casava 1.8 software.
3' adapter trimming with FastX-toolkit.
Library sorting based on sample barcode sequence with custom script.
Random barcode trimming with custom script.
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0.
Alignment with TopHat v2.0.9.
Read quantitation using custom scripts.
Genome_build: hg38
Supplementary_files_format_and_content: *txt: Text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts.

source_name: HEK293, siRNA eif5A

extract_protocol:
RNase I footprinting, ribosome pelleting, RNA extraction.
RNA extraction, preadenylated linker ligation, rRNA depletion, reverse transcription, cDNA circularization, PCR amplification for ribosome profiling.

tag: cell line

tag: sirna

value: Cycloheximide


title: d5A1n


title: DN_14_ATAC_Seq


title: DN_12_ATAC_Seq


title: GA-08_S22_ATAC_Seq


title: dCl2n

description:
Ribosome Profiling
processed data file: dCln.merge.1.txt

source_name: HEK293, siRNA control

value: control


title: dCl1n


title: DN_11_ATAC_Seq


title: disome_rep2, anisomycin

description: Ribosome Profiling

data_processing:
Library strategy: Ribo-seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: hg38
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

source_name: disome_rep2, anisomycin

extract_protocol: RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification for ribosome profiling

value: anisomycin

tag: genetic background

value: WT

tag: extracted molecule

value: total RNA

value: Rnase I footprinting, ribosome pelleting, RNA extraction


title: DN_09_ATAC_Seq


title: disome_rep1, anisomycin

description: Ribosome Profiling

source_name: disome_rep1, anisomycin


title: DN_08_ATAC_Seq


title: DN_07_ATAC_Seq


title: monosome_rep1

description: Ribosome Profiling

data_processing:
Library strategy: Ribo-Seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: hg38
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

extract_protocol:
Rnase I footprinting, ribosome pelleting, RNA extraction
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification for ribosome profiling

tag: genotype


title: disome_rep1

description: Ribosome Profiling


title: H3K4me2_early

city: New York

first: Iestyn

last: Whitehouse

state: New York

address: 1275 York Avenue

department: Molecular Biology

institute: Sloan-Kettering Institute

data_processing:
Raw .fastq files were aligned using bowtie2 and sorted for base quality using samtools
bedtools -genomecov was used to calculate hits per base from bam files-- signal scores were then normalized according to inverse of reference reads per million (RRPM) calculated using S. pombe alignment scores bowtie2
Individual sequencing reads in early embryo, gastrula, and late embryo replicates were annotated into peak calls using MACS (v2.1) (--broad peak call) (Zhang et al. 2008)
We considered high-confidence H3K27ac and H3K4me2 peaks to be those which were: consistent across replicate time points, detected by sonication and MNase assays, or supported by previously published C. elegans chromatin annotations
wig files were generated using a custom perl script, scores represent the normalized read counts, allowing comparison of libraries across embryo stages
Genome_build: WS235
Supplementary_files_format_and_content: wig file for each respective modification and embryo stage

organism: Caenorhabditis elegans

source_name: Embryonic cells

growth_protocol: Approximately 350,000 L1-stage egl-30(tg26) worms were grown to adulthood at 20°C on NGM plates until early embryos were detectable ex utero; embryos were bleached with sodium hypochlorite solution, washed with M9 buffer, and resuspended in aliquots of egg buffer

extract_protocol:
Staged embryos designated for ChIP-seq analysis were cross-linked with a 2% formadehyde solution (diluted in 500 mL M9 buffer) for 30 minutes, followed by the addition of 125 mM glycine to quench the reaction, and two final washes in PBS + protease inhibitors.  Extracts were prepared from synchronized egl-30(tg26) embryos by standard methods described previously (Reichsteiner et al. 2010, Ercan et al. 2007).  Approximately 2 mg of extract from each embryo stage was immunoprecipitated with 2 ug of commercially available antibodies previously cited in C. elegans chromatin studies
Extracted DNA was prepared into ChIP-seq libraries using the NEBNext Ultra DNA library preparation kit for Illumina (New England Biolabs) and was sequenced on the HiSeq 2500 platform

treatment_protocol: Proper embryo synchrony and developmental staging were visually confirmed by microscopy during each time-course experiment—developmental timing was validated by comparing mRNA transcripts in staged embryo populations to expected gene expression patterns from single-embryo studies (Hashimony et al. 2015)

tag: strain

tag: chip antibody

value: H3K4me2 (Abcam:ab7766)


title: disome_rep2

description: Ribosome Profiling


title: CN_18_ATAC_Seq

source_name: Glutmatergic, day-15 post induction

treatment_protocol: To prepare cortical neurons, NPCs were single-cell seeded into Geltrex-coated plate at 40,000 cells per cm2 on Day 0. From Day 0 to Day 14, NPCs were cultured in NeuralbasalPlus media with every other day media change. NeuralbasalPlus media was prepared as 490ml NeuralBasal, 1x B27Plus Supplement (Thermofisher), 1x Glutamax, 10 ng/ml BDNF (PeproTech), 10ng/ml GDNF (PeproTech), 10ng/ml NT-3 (PeproTech). Cells were harvested at day 15 for ATAC-Seq or RNA isolation.

value: iPS-derived Glutamatergic Neurons, day-15 post induction


title: CN_21_ATAC_Seq


title: CN_20_ATAC_Seq


title: H3K4me2_late


title: H3K27ac_gastrula

value: H3K27ac (Abcam:ab4729)


title: CN_19_ATAC_Seq


title: H3K4me2_gastrula


title: CN_16_ATAC_Seq


title: CN_17_ATAC_Seq


title: CN_14_ATAC_Seq


title: H3K27ac_late


title: CN_12_ATAC_Seq


title: CN_15_ATAC_Seq


title: CN_11_ATAC_Seq


title: Mock

city: Nanjing

first: zhisheng

last: wu

address: Immunology

department: Immunology

country: China

institute: Nanjing medical university

description: mock infected

data_processing:
FastQC softwae was used to filter the raw data and then got the clean data.
Hisat2 was used to map the clean data to the reference genome sequences
Stringtie software was used  to the assembly the reads that mapped the genome.
Stringtie software was used to calculate the expression amount readcount. Then calculate the FPKM of the gene and transcript.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Mock-infected HSB-2

growth_protocol: Mock-infected and HHV-6A-infected HSB-2 cells were cultured for 72 h

extract_protocol:
The totla RNA was extracted  for libraries construction by the Triozol kit according the standard protocol.
Libraries were prepared for sequencing using standard Illumina protocols

value: T lymphoblast

value: control; Mock-infected


title: HHV-6A

description: HHV-6A infected

source_name: HHV-6A-infected HSB-2

value: HHV-6A GS strain-infected


title: monosome_rep2

description: Ribosome Profiling


title: H3K27ac_early


title: CN_13_ATAC_Seq


title: CN_09_ATAC_Seq


title: CN_10_ATAC_Seq


title: CN_08_ATAC_Seq


title: CD44-negative 03

type: RNA

city: 江東区

first: Myungkyu

last: Jang

state: 東京都

department: Chemotherapy

institute: JFCR

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Gene-level expression signals were obtained by processing of raw data with the RMA procedure using GeneSpring GX (Agilent Technologies).

label: biotin

source_name: Human Colon Cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: The cell line was cultured in vitro in 10cm dishes until 80-90% confluency and then total RNA was isolated.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: no treatment

tag: cd44 status


title: CN_06_ATAC_Seq


title: CN_04_ATAC_Seq


title: CN_05_ATAC_Seq


title: COMBO, biological rep 3

city: Boston

first: Ryan

middle: P

last: Kuzmickas

state: MA

address: 77 Avenue Louis Pasteur, NRB458B

department: Genetics

institute: Brigham and Women's Hospital

description: gene expression data after DTE (24hr)

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA-normalized with Affymetrix Transcriptome Analysis Console (TAC) software

source_name: PC3 prostate cancer cells treated with COMBO (72hr)

label_protocol: standard Affymetrix protocol

growth_protocol: PC3 cells were cultured in RPMI media supplemented with 10% FBS, 1% Penicillin/Streptomycin

extract_protocol: RNA was isolated from PC3 cells 72 hours after treatment with indicated drugs. RNA was extracted using Trizol according to manufacturer’s protocol, followed by further purification with Qiagen Rneasy kit (74201)

treatment_protocol: PC3 cells were treated for 72 hours with vehicle (DMSO), 2uM vorinostat (VOR, HDACi), 5uM GSK126 (GSK126, EZH2i), or all both

value: human prostate cancer cell line


title: COMBO, biological rep 2

description: gene expression data after DTE (24hr)


title: GSK126, biological rep 3

description: gene expression data after E (24hr)

source_name: PC3 prostate cancer cells treated with GSK126 (72hr)


title: VOR, biological rep 3

description: gene expression data after DT (24hr)

source_name: PC3 prostate cancer cells treated with (72hr)


title: VOR, biological rep 1

description: gene expression data after DT (24hr)


title: CD44-negative 02


title: DMSO, biological rep 1

description: gene expression data after DMSO (24hr)

source_name: PC3 prostate cancer cells treated with DMSO (72hr)


title: VOR, biological rep 2

description: gene expression data after DT (24hr)


title: CD44-positive 02


title: DMSO, biological rep 2

description: gene expression data after DMSO (24hr)


title: CN_02_ATAC_Seq


title: CN_03_ATAC_Seq


title: CN_07_ATAC_Seq


title: GSK126, biological rep 1

description: gene expression data after E (24hr)


title: rA1-dCas12a-BE:VEG rep c

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

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 GRCh38/hg38 human or GRCm38/mm10 mouse reference genome using BWA-MEM 0.7.9a.
Genome_build: hg38 for human samples and mm10 for mouse samples
Supplementary_files_format_and_content: Excel for Indels and Base Subtitutions

source_name: HEK293T cells

growth_protocol: HEK293T and U2OS cells from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and regularly tested to exclude mycoplasma contamination.

extract_protocol:
For DNA, after 72 hr, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre) or the cells were lysed in 2× SDS loading buffer for western blot.
For DNA, DNA-seq libraries were prepared with NEB Next Ultra™ II  FS DNA Library Prep Kit. Targeted deep sequencing was performed on Illumina Hiseq X ten or NextSeq 500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: For base editing in genomic DNA, HEK293T and U2OS cells were seeded in a 24-well plate at a density of 1.6 × 105 per well and transfected with 200 μl serum-free Opti-MEM that contained 5.04 μl LIPOFECTAMINE LTX (Life, Invitrogen), 1.68 μl LIPOFECTAMINE plus (Life, Invitrogen), 1 μg dCpf1-BE expression vector (or hA3A-dCas12a-BE, hA3B-dCas12a-BE, hAID-dCas12a-BE, hA3AW98A-dCas12a-BE, hA3AW98Y-dCas12a-BE, hA3AW104A-dCas12a-BE, hA3AW104Y-dCas12a-BE, hA3AP134A-dCas12a-BE, hA3AP134Y-dCas12a-BE, hA3AW98Y/W104A-dCas12a-BE, hA3AW98Y/P134Y-dCas12a-BE, hA3AW104A/P134Y-dCas12a-BE, hA3AW98Y/W104A/P134Y-dCas12a-BE, hA3AW104A-dCas12a-BE-op, hA3AW104A/Y130F-dCas12a-BE-op, hA3AW104A/Y132D-dCas12a-BE-op, hA3AW98Y/W104A-dCas12a-BE-op, hA3AW98Y/W104A/Y130F-dCas12a-BE-op, hA3AW98Y/W104A/Y132D-dCas12a-BE-op, hA3AW104A/P134Y-dCas12a-BE-op, hA3AW104A/P134Y/Y130F-dCas12a-BE-op, hA3AW104A/P134Y/Y132D-dCas12a-BE-op and hA3AW98Y/W104A/Y130F/Y132D-dCas12a-BE-op expression vector) and 0.68 μg crRNA or sgRNA expression vector. After 72 hr, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre) or the cells were lysed in 2× SDS loading buffer for western blot.

tag: 5'-end trimming of r1

tag: 3'-end trimming of r1


title: CD44-positive 01


title: GSK126, biological rep 2

description: gene expression data after E (24hr)


title: CD44-negative 01


title: COMBO, biological rep 1

description: gene expression data after DTE (24hr)


title: ExVivo_Blood_No_Death [REA15133_SNS]

city: Valladolid

first: Pedro

last: Martinez-Paz

state: Valladolid

address: C/ Ramón y Cajal 7

country: Spain

institute: Faculty of Medicine

description: Gene expression of peripheral blood from patients who will not die before 90 days

hyb_protocol: Following “One-Colour microarray based Gene Expression Analysis protocol version 5.7” (Agilent p/n 4140-90040), 3 µg of labelled cRNA was hybridized with the Agilent Whole Human Genome Oligo Microarray Kit (Agilent p/n G2519F-014850).

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner Agilent G2565BA according to the manufacturer’s instructions.

data_processing: Raw files were read into R(limma package) by read.maimages for green only values. Background correction was performed by normexp(saddle) method, offset value=50. Then normalization between arrays was achieved by quantlile method. Repead probe names were aggregated by median values.

source_name: Peripheral Blood, No Death

label_protocol: 100 ng of purified total RNA was used to produce cyanine 3-CTP-labelled cRNA using the Quick Amp Label kit (Agilent p/n 5190-0442).

extract_protocol: Total RNA was extracted from blood samples using the PAX gene blood RNA System (Hombrechtikon, Switzerland). RNA was quantified by spectrometry (Nanodrop ND100, Nanodrop Technologies, Wilmington, Delaware). RNA was eluted with 80 µL of RNase-free H2O. RNA quality and concentration was measured by RNA Experion Bioanalyzer (BioRad, California USA) assay.

treatment_protocol: The samples were collected within the first 24 hours of ICU admission.

tag: subject group

value: patient who will not die before 90 days

tag: gender

value: Female

tag: tissue

value: Whole blood


title: DMSO, biological rep 3

description: gene expression data after DMSO (24hr)


title: hA3A(C106S)-dCas12a-BE:PD1 rep c;BEACON2:PDE, BLM rep c

value: hA3A(C106S)-dCas12a-BE and BEACON2


title: CD44-positive 03


title: ExVivo_Blood_Death [SS_65exp2]

description: Gene expression of peripheral blood from patients who will die before 90 days

source_name: Peripheral Blood, Death

value: patient who will die before 90 days

value: Male


title: ExVivo_Blood_No_Death [SS_116exp1]


title: ExVivo_Blood_No_Death [SIRS_36exp1]


title: hA3A(C106S)-dCas12a-BE:PD1repb;S6,S4,RUN,EMX,DYR,DNM,CDKrepc;BEACON1:PMS,PDE,PAF,CHD,BLMrepc;BE3:VEGrepc

description: hA3A(C106S)-dCas12a-BE:PD1 rep b;S6, S4, RUN, EMX, DYR, DNM, CDK rep c;BEACON1:PMS, PDE, PAF, CHD, BLM  rep c; BE3:VEG rep c

value: hA3A(C106S)-dCas12a-BE and hA3A(C106S)-dCas12a-BE and BEACON1 and BE3


title: ExVivo_Blood_Death [SS_77exp1]


title: hA3A(C106S)-dCas12a-BE:S6, S4, RUN, EMX, DYR, DNM, CDK rep b;BE2:VEG rep c

value: hA3A(C106S)-dCas12a-BE and BE2


title: hA3A(C106S)-dCas12a-BE:S6, S4, RUN, PD1, EMX, DYR, DNM, CDK rep a; YE1-BE3:SPA, PMS, PAF rep c

value: hA3A(C106S)-dCas12a-BE and YE1-BE3


title: hA3A(C101S)-dCas12a-BE:S6 rep c; BE2:SPA, PMS, PAF, BMR rep c

value: hA3A(C101S)-dCas12a-BE and BE2


title: hA3A(C101S)-dCas12a-BE:S4, RUN, PD1, EMX, DYR, DNM, CDK rep c;S6 rep b;BEACON2: PDE, BLM  rep b; SPA, BMR rep c

value: hA3A(C101S)-dCas12a-BE and hA3A(C101S)-dCas12a-BE and BEACON2 and BEACON2


title: YE1-BE3:PDE, CHD, BMR, BLM rep c; SPA, PMS, PAF rep b

value: YE1-BE3 and YE1-BE3


title: hA3A(C101S)-dCas12a-BE:S4, RUN, PD1, EMX, DYR, DNM, CDK rep b;BEACON1: PDE, PAF, CHD, BLM rep b; SPA, BMR rep c

value: hA3A(C101S)-dCas12a-BE and BEACON1 and BEACON1


title: hA3A(C101S)-dCas12a-BE:S6, S4, RUN, PD1, EMX, DYR, DNM, CDK rep a; rA1-dCas12a-BE: VEG rep b


title: BE2: PDE, CHD, BLM rep c; SPA, PMS, PAF rep b; BE3:VEG rep b

value: BE2 and BE2 and BE3


title: CHD9#WT2_E15_LIVER

city: Amsterdam

first: Anton

last: Berns

state: Amsterdam

address: Plesmanlann 121

department: Division of Molecular Genetics

country: Netherlands

institute: NKI

description: Embryonic (E15) brain and liver were isolated from littermates and snap-frozen

data_processing:
Illumina Casava1.7 software used for basecalling.
Tophat version: 2.1, HTSeq count (v0.5.3), DESeq2
Genome_build: mm9 (MEFs, ESCs), mm10 (ED15 brain and liver; EmuMyc  lymphomas), hg37 (K562 and SNB19 cells)
Supplementary_files_format_and_content: tab-delimited text files include raw read count values for each Sample

source_name: liver E15

extract_protocol:
Total RNA was extracted using Trizol, prepared using TruSeq protocol, and standard sample preparation protocols and RNA-seq was performed on a HiSeq2000 machine (Illumina) at the NKI Genomics Core Facility.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic liver

value: wild type


title: CHD9#WT1_E15_LIVER


title: ExVivo_Blood_Death [REA1565_SNS]


title: BEACON2:PDE rep a;SPA, BMR rep b; BE2:VEG BE2 rep b; Cas9:VEG rep c

value: BEACON2 and BEACON2 and BE2 and Cas9


title: BEACON1:PMS, PAF, CHD rep a; SPA, BMR rep b; Cas9:VEG rep b

value: BEACON1 and BEACON1 and Cas9


title: YE1-BE3:PDE, CHD, BMR, BLM rep b;SPA, PMS, PAF rep a


title: ExVivo_Blood_No_Death [SIRS_45exp1]

value: patient who will not die before 90 days


title: ExVivo_Blood_No_Death [SIRS_6exp2]

value: Whole blood


title: ExVivo_Blood_No_Death [REA17338_SNS]


title: ExVivo_Blood_Death [REA17427_SNS]

value: Female


title: BE2:PDE, CHD, BMR, BLM rep b; SPA, PAF rep a

value: BE2 and BE2


title: ExVivo_Blood_No_Death [SS_14exp2]

value: Male


title: ExVivo_Blood_Death [REA17443_SNS]

value: patient who will die before 90 days


title: ExVivo_Blood_No_Death [SS_105exp1]


title: BEACON2:SPA, BMR, BLM rep a; rA1-dCas12a-BE: VEG rep a

value: BEACON2 and rA1-dCas12a-BE


title: ExVivo_Blood_No_Death [REA17337_SNS]


title: ExVivo_Blood_No_Death [REA17267_SNS]


title: ExVivo_Blood_Death [REA17432]


title: BE3:VEG rep a


title: H3K27me3 WT

city: Milan

first: Chiara

last: Lanzuolo

address: Via Francesco Sforza 35

country: Italy

institute: CNR and Istituto Nazionale Genetica Molecolare

data_processing:
H3K27me3_WT
Basecalls performed using Phred33 quality score
Sequenced reads were trimmed for quality and adaptor sequence using Trimmomatic v0.32 with ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35 parameters in single-end mode
Trimmed reads were mapped to mm10 and dm6 genomes using Bowtie v1.0.1 with -m 1 parameter and PCR duplicates removed with samtools rmdup
Reads ambiguously mapping to both genomes were removed and the steps repeated for both mm10 and dm6 genomes
Genome_build: Genome_build: mm10, dm6
Supplementary_files_format_and_content: Supplementary_files_format_and_content: wiggle files with smoothed signal generated using spp R package

source_name: Muscle stem (satellite) cells_Lmna Δ8-11 +/+

extract_protocol:
Cells were sonicated and for spike-in experiments a 5% of sheared drosophila chromatin was added to each sample. Satellite cells from pools of 6-9 mice per genotype were used
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cell extraction protocol: Satellite cells were isolated from hind-limb muscle and fixed before sorting using FACS

tag: strain background

tag: genotype/variation

value: Lmna {delta}8-11 +/+

value: Post natal day 19

value: Muscle stem (satellite) cells

value: H3K27me3 (Millipore 07-449)


title: ExVivo_Blood_Death [REA17425]

tag: age


title: BEACON1:PMS rep b; SPA, PDE, BMR, BLM rep a

tag: treatment

value: BEACON1 and BEACON1


title: 12-month WT

first: Chang

last: Zhang

state: Shanghai

address: 320 Yue Yang Rd, Xuhui District

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The stat of mapped reads was list in w8-WT80.mapping_statistics(2-month WT), w8-HKO82.mapping_statistics(2-month HKO),M13-WT44.mapping_statistics(12-month WT),M13-HKO24.mapping_statistics(12-month nontumor),M13-tumor24.mapping_statistics(12-month tumor).
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: GRCm38

source_name: Liver

extract_protocol:
Liver tissues of w8-WT80,w8-HKO82,M13-WT44,M13-HKO24,M13-tumor24 were collected, and RNAs were harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: postnatal 12-month


title: 12-month nontumor


title: 12-month tumor


title: BE2:PMS, PDE, CHD, BMR, BLM rep a; Cas9:VEG rep a

tag: cell line

value: BE2 and Cas9


title: 2-month HKO

value: postnatal 2-month


title: YE1-BE3:PDE, CHD, BMR, BLM rep a; BE2:VEG rep a

value: YE1-BE3 and BE2


title: 2-month WT

value: wild type


title: ExVivo_Blood_Death [REA1567_SNS]

value: Whole blood


title: ExVivo_Blood_No_Death [SL_164expI]

value: patient who will not die before 90 days


title: ExVivo_Blood_No_Death [REA16217_SNS]

value: Female


title: hA3A(P134A)-dCas12a-BE:PD1, EMX, DNM rep c


title: ExVivo_Blood_No_Death [SS_138exp1]


title: ExVivo_Blood_No_Death [SS_94exp2]


title: GW3965 rep2

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Read quality filtering: Every read that was considered valid by the Illumina control software was processed and filtered as follows: a) any 3' bases with a quality score of 'B' were removed; b) if the read ended in a poly(A)-sequence leaving less than 25 transcript-derived bases, the read was discarded; c) if the remaining sequence consisted of less than six non-A bases, or a dinucleotide repeat with less than six other bases at either end, the read was discarded.
Alignment:the reads were aligned to the genome using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings for each read. Any reads with no alignments were re-aligned against an artifical chromosome, containing all possible splice junctions arising from the exons defined by the known transcript variants. Reads mapping within these splice junctions were translated back to the corresponding actual genomic positions. The UCSC transcript models were used for the expression level calculation. If a locus had several transcript variants, the exons of these were merged to a combined model that represented all expression from the locus. To account for incomplete cap site knowledge, the 5' ends of all models were extended by 100 bases, but not beyond the 3' end of any upstream nearby exon of another gene of the same orientation.
Annotation and quantitation:  Reads that had one or more repeat mappings that was outside exons, was assigned randomly as one of these repeats and contributed to the summarized read count of that repeat class. Else, if it had one or more mappings to exons, it was assigned randomly to one of the exons, even if the sequence was repeat-like. If it had no exon mapping, it was assigned randomly at one of the mappings. The expression level of each transcript model was taken as the total number of reads at all its possible mapping positions.
Genome_build: mm9
Supplementary_files_format_and_content: TAB-delimited file of raw read counts. Total counts of repeat classes are deisgnated by the prefix 'r_'

source_name: ventral midbrain neuospheres

extract_protocol:
The neurospheres were washed twice with cold-PBS before total RNA isolation with the RNeasy kit (Qiagen). The RNA integrity and concentration was checked using Qubit and 2200 TapeStation (Agilent)
An aliquot of 0,5μg of RNA was used for cDNA synthesis. Illumina Truseq libraries were prepared using corresponding kit and protocols from Illumina.

treatment_protocol: Neurospheres were expanded for three days and treated with the corresponding compounds or vehicle (DMSO) for 5h in N2 media.

tag: developmental stage

tag: background mouse strain


title: GW3965 rep1


title: hA3A(W104A)-dCas12a-BE:RUN rep f; RUN, PD1, EMX rep c


title: ExVivo_Blood_Death [SS_130exp1]

value: Male


title: ExVivo_Blood_No_Death [SS_80exp2]


title: GW3965+CT99021 rep2


title: GW3965 rep3


title: hA3A(W104Y)-dCas12a-BE:PD1 rep c


title: ExVivo_Blood_Death [SS_84exp2]

value: patient who will die before 90 days


title: ExVivo_Blood_No_Death [SIRS_51exp2]


title: CT99021 rep1


title: ExVivo_Blood_No_Death [SL_113expI]


title: CT99021 rep2


title: hA3A(W98Y)-dCas12a-BE:PD1, DNM rep c


title: Control rep3


title: Control rep2


title: hA3A(P134Y)-dCas12a-BE:RUN, DNM rep c


title: GW3965+CT99021 rep3


title: L7_CGATGT_Input_Vehicle

data_processing:
The ChIP-seq reads were analyzed for peak calling using HOMER base suite v4.3 and MACS 1.4.2.
The top 10% of the peaks were used for de novo motif finding using the MEME-ChIP tool from MEME suite with default settings and with HOMER based suite.
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle file, one for foward and one for reverse reads

source_name: cell line SN4741

extract_protocol:
DNA sequencing libraries were made using the kit from Illumina, except Illumina TruSeq adaptors were used to enable multiplexing.
ChIP-seq libraries were prepared using corresponding kit and protocols from Illumina

treatment_protocol: 80% confluent 15 cm dishes of the dopaminergic-like cell line SN4741 were treated with GW3965 2μM for 1.5h. The experiments were performed using 1μg of antibody against LRXs per IP

tag: antibody

value: vehicle


title: Control rep1


title: hA3A-dCas12a-BE: PD1 rep h; RUN rep e

value: hA3A-dCas12a-BE and hA3A-dCas12a-BE


title: ExVivo_Blood_Death [SS_101exp1]


title: hA3A(W98A)-dCas12a-BE:RUN, EMX rep c


title: GW3965+CT99021 rep1


title: ExVivo_Blood_No_Death [SNS_103_expI]


title: L4_ACTTGA_Input_Vehicle


title: L7_ATCACG_Chip_LXR_Vehicle

value: anti mouse LXR

tag: antibody vendor

value: non-commercial, made by and described in Jakobsson et al. 2009, PMID:19481530


title: hA3A(P134A)-dCas12a-BE:EMX, DNM rep b; RUN rep c


title: hA3A(P134Y)-dCas12a-BE:PD1, EMX  rep c; RUN rep b


title: L4_ATCACG_Chip_LXR_Vehicle


title: hA3A(W104Y)-dCas12a-BE:RUN, EMX, DNM rep c


title: 5mo_il34_2

city: Rotterdam

first: Laura

middle: Esmee

last: Kuil

address: Wytemaweg 30

institute: Erasmus MC

data_processing:
Sequencing and base-calling was performed on the Illumina hiseq 2500.
Resulting base-calls were de-multiplexed using the Illumina Casava 1.8 software.
Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used.
Abundance estimation was performed using cufflinks  v2.2.1 with both the frag-bias-correct and multi-read-correct flags set. The raw read counts were measured using HTSeq-count version 0.11.0. using the union setting.
The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges (Lawrence et al. Plos Computational Biology, 2013). Differential gene expression analysis was performed with Bioconductor package EdgeR (Robinson, et al., 2010).
Genome_build: GRCz10
Supplementary_files_format_and_content: CPM values [.csv] semicolon-delimited files.

organism: Danio rerio

source_name: whole fish

growth_protocol: HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf, from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf - 13 dpf. From 13 dpf onwards brine shrimps, paramecia and dry food

extract_protocol:
Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg-GFP+ cells were FAC-sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART-seq V4 ultra low input RNA kit for sequencing (Takara BIO USA, Inc.). Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end-sequenced (2x75 bp) on the Illumina HiSeq 2500.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 1,5 mpf

tag: strain

value: il34re03/re03 tg(mpeg-GFP)

tag: cell type

value: mpeg-GFP+ cells


title: ExVivo_Blood_Death [SS_25exp2]


title: 5mo_il34_3


title: 5mo_il34_1


title: L7_TGACCA_Input_GW3965

value: GW3965 for 1.5 hours


title: ExVivo_Blood_Death [SS_64exp1]


title: ExVivo_Blood_Death [SIRS_72exp1]


title: ExVivo_Blood_Death [SS_24exp2]


title: L4_GGCTAC_Input_GW3965


title: hA3A(W98Y)-dCas12a-BE:RUN rep c


title: 5mo_csf1rdm_2


title: L4_TAGCTT_Chip_LXR_GW3965


title: hA3A-dCas12a-BE:DNM rep h; EMX rep g


title: ExVivo_Blood_Death [SS_76exp1]


title: hA3A(W98A)-dCas12a-BE:PD1, DNM rep c


title: 5mo_control_3

value: wildtype tg(mpeg-GFP)


title: hA3A(P134Y)-dCas12a-BE:EMX, DNM rep b


title: 5mo_control_2


title: ExVivo_Blood_No_Death [SIRS_63exp1]


title: hA3A(W104A)-dCas12a-BE:PD1, EMX rep b


title: ExVivo_Blood_No_Death [SIRS_62exp1]


title: 5mo_csf1rdm_3


title: ExVivo_Blood_Death [SIRS_60exp1]


title: 5mo_control_1


title: ExVivo_Blood_No_Death [SIRS_57exp1]


title: hA3A(W104Y)-dCas12a-BE:EMX, DNM rep b


title: L7_TTAGGC_Chip_LXR_GW3965


title: Saline 2.2

city: San Antonio

first: Daniel

middle: J

last: Lodge

state: Bexar

address: 7703 Floyd Curl Drive

department: Pharmacology

institute: UNIVERSITY OF TEXAS HLTH SCI CTR SAN ANTONIO

description: Sample 23

data_processing:
In Partek Flow, input paired fastq files were trimmed by quality at both ends using phred 30 and minimum read length of 25 as cutoffs (Trim Bases tool).
Quality reads were aligned to the RefSeq rn6 genome (Rattus norvegicus) with the STAR v2.4.1d aligner using default parameters for a mammalian genome.
Aligned reads were quantified (Quantify to Annotation Model Partek E/M tool) against RefSeq rn6 Transcripts 80 (2017-02-06) and resulting counts were normalized by sample to TPM (Total per million) with an offset of 0.0001 (Normalize Counts tool).
Normalized reads were used for GSA (Gene Specific Analysis tool) of differential expression at gene and transcript levels.
For differential expression analysis, genes were included if the lowest average coverage (normalized read count) by treatment group was greater than 1.0 and if they were within the estimation reliability cutoff defined by the Partek software.
Genome_build: rn6
Supplementary_files_format_and_content: counts and differential expression results

organism: Rattus norvegicus

source_name: hippocampus and neocortex

growth_protocol: Timed pregnant female Sprague-Dawley rats were obtained from Envigo on gestational day 11.

extract_protocol:
RNA was extracted using the Qiagen AllPrep kit. Briefly, 17-75mg of tissue were homogenized in 600-2,400ul RLT buffer, and then processed through the AllPrep kit following manufacturer’s instructions. RNA samples were then DNase treated using the TurboDNA-free kit (Thermo Fisher Scientific) and cleaned with the Zymo RNA Clean and Concentrator kit.
250ng of RNA underwent cDNA library preparation using the Illumina TruSeq Stranded mRNA kit, followed by cluster generation and sequencing (2x100bp paired end read) on the Illumina HiSeq 2500.

treatment_protocol: Either polyinosine:cytosine (Poly I:C, 7.5 mg/kg, i.p), methylazoxymethanol acetate (MAM: 22mg/kg, i.p.) or saline were administered on gestational day 17. For maternal protein malnutrition, pregnant rats had access to a low protein diet ad libitum (Envigo: TD.90016) containing 6.1% protein, 75.6% carbohydrate and 5.5% fat (3.8Kcal/g) from GD11-GD18. Control rats were fed an isocaloric diet of 20.3% protein, 61.6% carbohydrate and 5.5% fat (3.8Kcal/g: Envigo: TD.91352) from GD11-GD18. Pregnant rats were sacrificed on GD18 (18 hours following drug administration),

value: embryonic day 18

tag: maternal treatment

value: Saline

value: hippocampus and neocortex


title: Saline 2.1

description: Sample 22


title: hA3A(P134A)-dCas12a-BE:RUN rep b

tag: 5'-end trimming of r1


title: Saline 2.3

description: Sample 24


title: ExVivo_Blood_No_Death [SS_137exp1]

value: Whole blood


title: hA3A(W98Y)-dCas12a-BE:EMX rep c; PD1 rep b

tag: 3'-end trimming of r1


title: 33dpf_csf1rdm_1

value: 33 dpf


title: Saline 1.3

description: Sample 21


title: ExVivo_Blood_No_Death [SIRS_68exp1]

tag: subject group

value: patient who will not die before 90 days


title: Saline 1.2

description: Sample 20


title: ExVivo_Blood_Death [SS_56exp1]

tag: gender

value: Female


title: 33dpf_csf1rdm_2


title: hA3A(W98A)-dCas12a-BE:RUN rep b


title: Poly I:C 2.3

description: Sample 18

value: Poly I:C

tag: tissue


title: 33dpf_control_2


title: 33dpf_control_3


title: hA3A(W104A)-dCas12a-BE:DNM rep c; PD1 rep a; RUN rep b, e

value: hA3A(W104A)-dCas12a-BE and hA3A(W104A)-dCas12a-BE and hA3A(W104A)-dCas12a-BE and hA3A(W104A)-dCas12a-BE


title: hA3A(P134Y)-dCas12a-BE:DNM rep a; PD1 rep b


title: hA3A-dCas12a-BE:PD1 rep g; PD1, EMX rep f; RUN rep d, i

value: hA3A-dCas12a-BE and hA3A-dCas12a-BE and hA3A-dCas12a-BE and hA3A-dCas12a-BE


title: Poly I:C 2.1

description: Sample 16


title: 33dpf_control_1


title: 5mo_csf1rdm_1


title: hA3A(P134A)-dCas12a-BE:PD1 rep b; RUN rep a


title: 33dpf_csf1rdm_3


title: Saline 1.1

description: Sample 19


title: hA3A(W104Y)-dCas12a-BE:EMX, DNM rep a; RUN, PD1 rep b


title: ExVivo_Blood_No_Death [SIRS_43exp1]

value: Male


title: ExVivo_Blood_No_Death [SIRS_67exp1]


title: csf1r_doubleknockout2_50hpf

source_name: whole embryos

growth_protocol: HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle

extract_protocol:
35 embryos (28 hpf wt, 50 hpf wt, 28 hpf csf1rdm) or 70 embryos (csf1rdm 50 hpf) were pooled per replicate sample and dissociated with trypsin on ice. mpeg-GFP+ cells were FAC-sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART-seq V4 ultra low input RNA kit for sequencing (Takara BIO USA, Inc.). Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end-sequenced (2x75 bp) on the Illumina HiSeq 2500.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 50 hpf


title: ExVivo_Blood_No_Death [SIRS_32exp1]


title: hA3A(W104A)-dCas12a-BE:DNM rep b; RUN rep d; RUN, EMX rep a

value: hA3A(W104A)-dCas12a-BE and hA3A(W104A)-dCas12a-BE and hA3A(W104A)-dCas12a-BE


title: Poly I:C 1.3

description: Sample 15


title: Poly I:C 1.2

description: Sample 14


title: ExVivo_Blood_Death [SIRS_78exp1]

value: patient who will die before 90 days


title: Poly I:C 2.2

description: Sample 17


title: Poly I:C 1.1

description: Sample 13


title: hA3A(W98Y)-dCas12a-BE:RUN, EMX, DNM rep b


title: wildtype_cntr3_50hpf

value: mpeg-GFP+ cells


title: MAM 2.3

description: Sample 12

value: MAM


title: ExVivo_Blood_No_Death [SS_12exp1]


title: MAM 2.2

description: Sample 11


title: csf1r_doubleknockout3_50hpf


title: wildtype_cntr2_50hpf

value: wildtype tg(mpeg-GFP)


title: hA3A(W98A)-dCas12a-BE:PD1, EMX, DNM rep b; RUN rep a


title: hA3A-dCas12a-BE:DNM rep f; EMX rep e

value: hA3A-dCas12a-BE and hA3A-dCas12a-BE


title: MAM 2.1

description: Sample 10

value: embryonic day 18


title: hA3A(P134A)-dCas12a-BE:PD1, EMX, DNM rep a


title: csf1r_doubleknockout2_28hpf

value: 28 hpf


title: csf1r_doubleknockout3_28hpf


title: csf1r_doubleknockout1_28hpf


title: ExVivo_Blood_Death [SS_4exp1]

value: Whole blood


title: ExVivo_Blood_No_Death [SIRS_16exp1]


title: ExVivo_Blood_No_Death [REA16238_SNS]


title: ExVivo_Blood_No_Death [SIRS_22exp1]


title: hA3A(W104Y)-dCas12a-BE:RUN, PD1 rep a


title: ExVivo_Blood_No_Death [SIRS_26exp1]


title: ExVivo_Blood_No_Death [SIRS_17exp1]


title: csf1r_doubleknockout1_50hpf


title: wildtype_cntr3_28hpf


title: ExVivo_Blood_No_Death [SS_9exp1]


title: MAM 1.1

description: Sample 7

value: hippocampus and neocortex


title: hA3A(W104A)-dCas12a-BE:DNM rep a


title: hA3A(W98Y)-dCas12a-BE:RUN, PD1, EMX, DNM rep a


title: Low Protein 2.2

description: Sample 5

value: Low Protein


title: wildtype_cntr2_28hpf


title: wildtype_cntr1_50hpf


title: hA3A(W98A)-dCas12a-BE:PD1, EMX, DNM rep a


title: MAM 1.3

description: Sample 9


title: hA3A(P134Y)-dCas12a-BE:RUN, PD1, EMX rep a


title: ExVivo_Blood_No_Death [SIRS_42exp1]

value: patient who will not die before 90 days


title: hA3A-dCas12a-BE:DNM rep i; EMX rep d; PD1 rep e

value: hA3A-dCas12a-BE and hA3A-dCas12a-BE and hA3A-dCas12a-BE


title: ExVivo_Blood_No_Death [SIRS_3exp1]

value: Female


title: Low Protein 1.3

description: Sample 3


title: hA3A(W98Y/W104A/P134Y)-dCas12a-BE:S6, RUN, PD1, EMX, DYR  rep c


title: Low Protein 2.3

description: Sample 6


title: MAM 1.2

description: Sample 8


title: wildtype_cntr1_28hpf


title: ExVivo_Blood_No_Death [SIRS_23exp1]


title: ExVivo_Blood_No_Death [SIRS_27exp1]


title: hA3A(W104A/P134Y)-dCas12a-BE:PD1, DNM rep c


title: Low Protein 1.1

description: Sample 1


title: ExVivo_Blood_Death [SNS_127_expI]


title: CT99021 rep3


title: hA3A-dCas12a-BE:DYR rep g; S4 rep i


title: ExVivo_Blood_No_Death [SIRS_33exp1]


title: ExVivo_Blood_No_Death [SIRS_31exp1]


title: ExVivo_Blood_Death [REA16260_SNS]


title: ExVivo_Blood_No_Death [SL_67expII]


title: hA3A(W98Y/P134Y)-dCas12a-BE:EMX, DYR, DNM, CDK rep b; PD1 rep c


title: Low Protein 2.1

description: Sample 4


title: hA3A(W98Y/W104A)-dCas12a-BE:S4, DNM rep b


title: hA3A-dCas12a-BE: S4 rep h


title: ExVivo_Blood_No_Death [SS_20exp2]


title: ExVivo_Blood_No_Death [REA1555_SS]


title: ExVivo_Blood_No_Death [SIRS_20exp1]


title: ExVivo_Blood_Death [SS_77exp2]


title: hA3A(W98Y/W104A)-dCas12a-BE:S6, S4, EMX, DYR, DNM rep c


title: ExVivo_Blood_No_Death [REA159_SS]


title: ExVivo_Blood_Death [SS_24exp1]


title: ExVivo_Blood_No_Death [SS_81exp2]


title: LO_d60 control, rep1

city: Baltimore

first: Shaun

middle: Michael

last: Kunisaki

state: MD

address: 1800 Orleans St, Suite 7353

department: Pediatric Surgery

institute: Johns Hopkins University

description: Lung organoids 60 days in culture

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Human Gene ST 2.1 plate, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592).

scan_protocol: Peg Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592).

data_processing: Normalized expressions by robust multiple-array averages were plotted using the heatmap.2 function from the gplots package in R (www.r-project.org) using default parameters. Transcriptome Analysis Console 4.0 was used for analysis.

source_name: Human LO 60div control patient

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: iPSCs were treated with 100 ng/mL Activin A and then incubated in foregut media: DMEM/F12 containing 1x N2 and 1x B27, 10 mM HEPES, 200 ng/mL Noggin, 10µM SB431542, 2µM Chiron, 500 ng/mL FGF4, and 1µM SAG for 8 days. Cells (25 organoids/well) were resuspended in 50 µL Matrigel and maintained in a 24-well plate with 500 ng/mL FGF10 until the study endpoint of 20, 40, or 60 days.

extract_protocol: RNA was extracted using a MagMAX-96 Total RNA Isolation Kit and MAG Max Express according to manufacturer's instructions

tag: tissue/cell type

value: lung organoids


title: Fetal_Lung_normal

description: Human fetal lung specimen

source_name: Human fetal lung control patient

value: fetal lung


title: LO_d60 CDH, rep1

description: Lung organoids 60 days in culture

source_name: Human LO 60div CDH patient


title: hA3A(W98Y/W104A/P134Y)-dCas12a-BE:DNM  rep c; S6, RUN, DYR rep b


title: LO_d40 CDH, rep2

description: Lung organoids 40 days in culture

source_name: Human LO 40div CDH patient


title: hA3A(W104A/P134Y)-dCas12a-BE: S6, S4, RUN, EMX rep c


title: hA3A(W98Y/P134Y)-dCas12a-BE:EMX, DNM, CDK  rep a; S4 rep c; S6, RUN, PD1 rep b

value: hA3A(W98Y/P134Y)-dCas12a-BE and hA3A(W98Y/P134Y)-dCas12a-BE and hA3A(W98Y/P134Y)-dCas12a-BE


title: LO_d40 control, rep1

description: Lung organoids 40 days in culture

source_name: Human LO 40div control patient


title: hA3A(W98Y/W104A/P134Y)-dCas12a-BE:PD1, DNM  rep b; S4, CDK rep c


title: LO_d40 CDH, rep1

description: Lung organoids 40 days in culture


title: ExVivo_Blood_No_Death [SIRS_28exp1]


title: ExVivo_Blood_No_Death [SS_151exp1]

value: Male


title: LO_d40 control, rep2

description: Lung organoids 40 days in culture


title: ExVivo_Blood_No_Death [SS_44exp1]


title: hA3A(W98Y/W104A)-dCas12a-BE:EMX, DYR rep b; RUN, PD1, CDK rep c; S4, DNM rep a

value: hA3A(W98Y/W104A)-dCas12a-BE and hA3A(W98Y/W104A)-dCas12a-BE and hA3A(W98Y/W104A)-dCas12a-BE


title: LO_d20 CDH, rep2

description: Lung organoids 20 days in culture

source_name: Human LO 20div CDH patient


title: hA3A(W104A/P134Y)-dCas12a-BE:DYR, CDK rep c; S6, RUN, PD1, EMX, DNM rep b

source_name: HEK293T cells


title: LO_d20 control, rep2

description: Lung organoids 20 days in culture

source_name: Human LO 20div control patient


title: hA3A(W98Y/W104A/P134Y)-dCas12a-BE:S4, EMX, CDK rep b; S6, PD1, DNM rep a


title: hA3A-dCas12a-BE: RUN rep f; S6, DYR rep i; hA3A(W98Y/W104A)-dCas12a-BE: S6 rep b

value: hA3A-dCas12a-BE and hA3A(W98Y/W104A)-dCas12a-BE and hA3A-dCas12a-BE


title: hA3A(W104A/P134Y)-dCas12a-BE:DNM rep a; S4, DYR, CDK rep b


title: hA3A(W98Y/P134Y)-dCas12a-BE:S6, RUN, EMX, DYR, DNM, CDK rep c


title: LO_d20 CDH, rep1

description: Lung organoids 20 days in culture


title: hA3A(W98Y/P134Y)-dCas12a-BE:S4 rep b and S6, RUN, PD1, DYR rep a


title: ExVivo_Blood_Death [REA1521_SS]

source_name: Peripheral Blood, Death

value: patient who will die before 90 days


title: LO_d20 control, rep1

description: Lung organoids 20 days in culture


title: IPS CDH, rep1

description: Undifferentiated iPS

source_name: Human iPS CDH patient

growth_protocol: iPS were derived from amniotic fluid cells expanded in [D/F12+10%FBS+Pen/Strep] medium, by transduction with Sendai virus encoding for OCT4, SOX2, KLF4, and cMYC transcription factors. At day 6, the cells were split and placed on irradiated mouse embryonic fibroblast feeder layers. Cells were cultured in human ES conditioned medium with 4 ng/mL of FGF-2. Individual colonies derived from MSCs were subsequently picked and propagated on Matrigel with mTeSR medium.

value: iPS


title: hA3A(W98Y/W104A)-dCas12a-BE:EMX, DYR rep a;RUN, PD1, CDK rep b


title: ExVivo_Blood_No_Death [SIRS_44exp2]

source_name: Peripheral Blood, No Death


title: IPS CDH, rep2

description: Undifferentiated iPS


title: hA3A(W98Y/W104A/P134Y)-dCas12a-BE:S4, RUN, EMX, DYR, CDK rep a


title: ExVivo_Blood_Death [SS_142exp1]


title: IPS control, rep1

description: Undifferentiated iPS

source_name: Human iPS control patient


title: ExVivo_Blood_No_Death [REA17435]


title: IPS control, rep2

description: Undifferentiated iPS


title: hA3A(W104A/P134Y)-dCas12a-BE:S6, S4, RUN, PD1, EMX, DYR, CDK rep a


title: hA3A(W98Y/P134Y)-dCas12a-BE:S4 rep a


title: ExVivo_Blood_No_Death [SIRS_61exp1]


title: hA3A(W98Y/W104A)-dCas12a-BE:S6, RUN, PD1, CDK rep a


title: ExVivo_Blood_Death [REA1542_SS]


title: Fibroblast CDH, rep1

description: In vitro expanded patient fibroblasts

source_name: Human fibroblast CDH patient

growth_protocol: Foreskin isolated fibroblasts were expanded in [D/F12+10%FBS+Pen/Strep] medium

value: fibroblasts


title: hA3A-dCas12a-BE: EMX rep h; S4, DNM rep g

value: hA3A-dCas12a-BE and hA3A-dCas12a-BE


title: hA3A-dCas12a-BE:PD1, EMX rep i


title: Fibroblast control, rep2

description: In vitro expanded patient fibroblasts

source_name: Human fibroblast control patient


title: ExVivo_Blood_Death [REA16243_SNS]


title: hA3A(P134Y)-dCas12a-BE:DYR rep c


title: Fibroblast CDH, rep2

description: In vitro expanded patient fibroblasts


title: hA3A(W104Y)-dCas12a-BE:S4, DYR  rep c


title: dCas9-KRAB_nosg_rep3

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Adapter sequences and low quality reads were trimmed uisng Trim Galore with "--illumina --fastqc -q 20 --stringency 3 --length 20".
Reads were then aligned to hg38 genome using bowtie2 (version 2.3.3.1) with "--end-to-end --sensitive".
Low-quality alignments and PCR duplicates were removed using samtools and Picard MarkDuplicates.
Gene expression was counted using htseq-count with "-s no -m union -t exon".
Genome_build: Human (hg38)
Supplementary_files_format_and_content: tab-delimited text files include gene expression count values for each Sample

growth_protocol: Protocol was according to ATCC.

extract_protocol:
RNA was extracted using TRIzol Reagent (cat# 15596018; ThermoFisher).
Library was constructed at CCHMC DNA Sequencing and Genotyping Core.

treatment_protocol: H441 cells were infected with a lentiviral vector carrying dCas9-KRAB with or without the sgRNA and then selected by puromycin (10 ug/ml).

value: lung papillary adenocarcinoma cells

tag: genotype

value: dCas9 only


title: hA3A(P134A)-dCas12a-BE:S6, S4, DYR rep c


title: dCas9-KRAB_sgTGFB1_B9D2_rep2

value: dCas9 w/sgTGFB1_B9D2


title: dCas9-KRAB_nosg_rep1


title: dCas9-KRAB_sgTGFB1_B9D2_rep3


title: ExVivo_Blood_No_Death [SL_37expII]

tag: age

value: Whole blood


title: ExVivo_Blood_Death [SS_92exp2]


title: Fibroblast control, rep1

description: In vitro expanded patient fibroblasts


title: dCas9-KRAB_sgTGFB1_B9D2_rep1


title: ExVivo_Blood_No_Death [REA17294_SNS]

value: patient who will not die before 90 days


title: ExVivo_Blood_No_Death [SIRS_18exp2]


title: dCas9-KRAB_nosg_input_rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Adapter sequences and low quality reads were trimmed uisng Trim Galore with "--illumina --fastqc -q 20 --stringency 3 --length 20".
Reads were then aligned to hg38 genome using bowtie2 (version 2.3.3.1) with "--end-to-end --sensitive".
Low-quality alignments and PCR duplicates were removed using samtools and Picard MarkDuplicates.
MACS2 software (version 2.1.0) was used for ChIP-seq peak calling. dCas9 peaks were called using “macs2 callpeak -t dCas9_ab.bam -c input.bam -f BAM -g hs -B --keep-dup 1 -q 0.01”; and H3K9me3 peaks were called with “macs2 callpeak -t H3K9me3_ab.bam -c input.bam -f BAM -g hs -B --keep-dup 1 --broad --broad-cutoff 0.1 -p 0.05”.
Genome_build: Human (hg38)
Supplementary_files_format_and_content: bdg files were bedGraph files generated by MACS2 callpeak function (version 2.1.0) for each comparison. Each file has four columns: chr, start, end, score. Scores represent the treatment fragment pileup or control lambda values scaled to the same depth.

extract_protocol:
ChIP was performed using a ChIP kit (cat# 9003; Cell Signaling Technology).
Library was constructed at CCHMC DNA Sequencing and Genotyping Core.

tag: chip antibody


title: ExVivo_Blood_Death [REA16251_SS]


title: ExVivo_Blood_No_Death [SIRS_31exp2]


title: hA3A(W98A)-dCas12a-BE:DYR rep c

tag: cell line

tag: treatment


title: dCas9-KRAB_nosg_input_rep1


title: LO_d60 CDH, rep2

description: Lung organoids 60 days in culture


title: hA3A(P134Y)-dCas12a-BE:S6, S4 rep c


title: Low Protein 1.2

description: Sample 2

value: embryonic day 18

value: Low Protein

value: hippocampus and neocortex


title: ExVivo_Blood_No_Death [REA1512_SS]

value: Female


title: Cas9_(Ab)_dCas9-KRAB_nosg_ChIPSeq_rep2

value: Cas9 (Active Motif cat# 61757)


title: hA3A(W104A)-dCas12a-BE:S4 rep c,f


title: Cas9_(Ab)_dCas9-KRAB_nosg_ChIPSeq_rep1


title: H3K9me3 (Ab)_dCas9-KRAB_nosg_ChIPSeq_rep2

value: H3K9me3 (Abcam cat# ab8898)


title: hA3A-dCas12a-BE:DYR rep f


title: hA3A(W104Y)-dCas12a-BE:S6 rep c


title: H3K9me3_(Ab)_dCas9-KRAB_nosg_ChIPSeq_rep1


title: SCN AncBE4max mouse embryo#14

source_name: Mouse embryos

value: mouse embryos


title: hA3A(W98Y)-dCas12a-BE:DYR rep c


title: hA3A(W104A)-dCas12a-BE:DYR rep c


title: ExVivo_Blood_No_Death [SIRS_15exp1]

value: Male


title: dCas9-KRAB_sgTGFB1_B9D2_input_rep1


title: hA3A(P134Y)-dCas12a-BE:CDK  rep c


title: SCN AncBE4max mouse embryo#13


title: hA3A(P134A)-dCas12a-BE:CDK rep c


title: SCN AncBE4max mouse embryo#12


title: Cas9_(Ab)_dCas9-KRAB_sgTGFB1_B9D2_ChIPSeq_rep2


title: SCN AncBE4max mouse embryo#15


title: ExVivo_Blood_No_Death [SIRS_28exp2]


title: SCN AncBE4max mouse embryo#11


title: Cas9_(Ab)_dCas9-KRAB_sgTGFB1_B9D2_ChIPSeq_rep1


title: dCas9-KRAB_sgTGFB1_B9D2_input_rep2


title: SCN AncBE4max mouse embryo#10


title: H3K9me3_(Ab)_dCas9-KRAB_sgTGFB1_B9D2_ChIPSeq_rep2


title: ExVivo_Blood_No_Death [SIRS_33exp2]


title: SCN AncBE4max mouse embryo#9


title: ExVivo_Blood_No_Death [SNS_55_expI]


title: SCN AncBE4max mouse embryo#8


title: LNCaP: E_LY

city: Houston

first: Anders

middle: Mikael

last: Strom

state: Texas

address: 3517 Cullen Blvd Bldg 545 room 3018

department: Biology & Biochemistry

institute: University od Hpuston

data_processing:
Alignment: STAR (v2.5), default parameters
Transcript assembly/quantification: HTSeq (v0.6.1), default parameters
Differential expression analysis: DESeq2 (1.24.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: .xlsx files contain transcript abundances and FPKM values

molecule: polyA RNA

source_name: AR-positive LNCaP PCa cells

growth_protocol: LNCaP cells grown to 60% confluency, media changed to RPMI 1640 + 10% DCC

extract_protocol:
RNA was extracted using RNeasy  kit from Qiagen according to protocol
Poly(A) mRNA was isolated using NEBNext poly(A) mRNA Magnetic Isolation Module. Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: Treatment with  DMSO, E2 10nM, or LY3201 1uM was for 24 hours

value: prostate

value: prostate cancer


title: hA3A(W98Y)-dCas12a-BE:S6, S4, CDK  rep c


title: ExVivo_Blood_No_Death [SS_56exp2]


title: ExVivo_Blood_No_Death [SL_3expII]


title: hA3A(W98A)-dCas12a-BE:S6, S4, CDK rep c


title: hA3A(W104Y)-dCas12a-BE:CDK rep c


title: hA3A(W104A)-dCas12a-BE:S4 rep b; S4 rep e; S6, CDK rep c

value: hA3A(W104A)-dCas12a-BE and hA3A(W104A)-dCas12a-BE and hA3A(W104A)-dCas12a-BE


title: ExVivo_Blood_No_Death [SS_80exp1]


title: ExVivo_Blood_No_Death [SIRS_19exp2]


title: ExVivo_Blood_No_Death [REA16254_SNS]


title: ExVivo_Blood_No_Death [SS_14exp1]


title: ExVivo_Blood_No_Death [REA16173_SS]


title: ExVivo_Blood_No_Death [SS_5exp1]


title: hA3A-dCas12a-BE: CDK rep I; DYR rep e; S4 rep f

value: hA3A-dCas12a-BE and hA3A-dCas12a-BE and hA3A-dCas12a-BE


title: SCN AncBE4max mouse embryo#7


title: ExVivo_Blood_Death [SL_42expII]

value: patient who will die before 90 days


title: ExVivo_Blood_Death [REA17277]


title: LNCaP: E_E2


title: hA3A(W104A)-dCas12a-BE: DYR rep b


title: SCN AncBE4max mouse embryo#6


title: ExVivo_Blood_Death [REA16248_SS]


title: LNCaP: E_DMSO


title: H3K9me3_(Ab)_dCas9-KRAB_sgTGFB1_B9D2_ChIPSeq_rep1

value: lung papillary adenocarcinoma cells


title: SCN AncBE4max mouse embryo#5


title: LNCaP: C_LY


title: ExVivo_Blood_No_Death [SL_145expI]


title: ExVivo_Blood_Death [SS_1exp2]


title: SCN AncBE4max mouse embryo#4


title: hA3A(W104Y)-dCas12a-BE:S6, S4, DYR, CDK rep b


title: hA3A(P134A)-dCas12a-BE:S6, S4, DYR, CDK rep b


title: hA3A(P134Y)-dCas12a-BE:S6, S4, DYR, CDK rep b


title: ExVivo_Blood_No_Death [REA15161_SS]


title: hA3A(W104A)-dCas12a-BE:S4 rep a; S6, CDK rep b; S6, S4 rep d


title: CRISPRi-scRNA-Seq (NPC_08)

first: Jubao

last: Duan

institute: NorthShore University HealthSystem

description: barcoded mRNA

data_processing:
*I1_001.fastq.gz: contains the 8 nt sample index.
*R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 98 nt RNA sequence.
10x Genomics cellranger v2.1.2 was used in pre-processing of raw sequencing data. Briefly, sequencing data were aligned to the human GRCh38/hg38 genome with spike-in gRNA sequence as artificial chromosomes (20 bp gRNA sequence and 250 bp downstream plasmid backbone). The full sequence of CROPSeq-Guide-Puro construct was also included as a spike-in chromosome to capture vector-borne sequences. The alignment was performed using STAR 2.5.1 and a spiked-in version of Gencode v28 GTF file as annotations. Gene count matrix (in HDF5 format) were used in subsequent R analysis. In all, we achieved a total mapping rate of 94.1%, with 74.4% mapping rate to the human transcriptome.
The cellrangerR package (2.1) was used to extract information and assemble data tables from the HDF5 files and generate the digital gene expression matrix, which was constructed based on deduplicated per-gene UMI. Cells with more than 500 genes and 11,000 UMIs detected were retained (4,099 out of 4,144 cells). For each cell, the mean read count was 109,945, and the median of UMI is 28,480, which translated to a median of 4,935 genes per cell. Subsequently, uniquely assigned cells were defined by the UMI count if their dominant gRNA was at least three times more than the sum of UMI counts from all other gRNAs. Such filters left 2,522 cells (60.8%) as uniquely assigned for further study. T-SNE analysis was performed using the in-built function of the cellrangerR package and subsequently plotted using R package ggplot2.
Differential expression (DE) analysis of single cells was performed using the edgeR package by applying a general linear model (glm) to the dataset and identify DE genes using QLF test with FDR < 0.05(45). While each sequence is targeted by 3 gRNAs, we find that often gRNAs have heterogeneous effects, so we analysed each gRNA separately. Cells with at least one read mapped to the gRNA of interest, but no reads mapped to other gRNAs are treated as cases. Cells with at least one read mapped to any of three negative control RNA and no reads mapped to other gRNAs are treated as controls. Only genes with CPM > 30 in more than 20% of cells are kept for DE analysis. For DE analysis for each gRNA, to correct for p-value inflation, we performed permutations by switching the label of cells (cases or controls) 30 times. We then used p values from all genes included in the permutations as the null distribution. We then used this null distribution to assign empirical p-value of each gene, as the number of genes with p values less than or equal to the observed test statistic in the null distribution divided by the total number of genes in the null distribution.
Genome_build: GRCh38
Supplementary_files_format_and_content: sparse count matrix

source_name: Neural progenitor cell

growth_protocol: NPC are prepared using PSC Neural Induction Medium (Thermofisher) following vendor’s protocol with modifications except for lines CD0000017 & CD0000020. Briefly, hiPSCs were replated as clumps in mTeSR media (STEMCELL) supplemented with 5 µM ROCK inhibitor (R&D Systems) on Day 0. From Day 1 to Day 9, cells were treated in PSC Neural Induction Medium with daily media change and routinely removal of differentiated non-neuron cells. PSC Neural Induction Medium was prepared as 490ml Neurobasal Medium (Thermofisher) and 10 ml Neural Induction Supplement (Thermofisher). On Day 10, P0 NPCs were ready for passaging. From P0 to P3, NPCs were passaged using Rosette Selection Reagent (STEMCELL) and expanded in Neural Expansion Medium. Media could be changed every other day after switching to Neural Expansion Medium. Neural Expansion Medium was prepared as 245 ml Neurobasal Medium, 245 ml Advanced DMEM⁄F-12 media (Thermofisher) and 10ml Neural Induction Supplement. From P4, NPCs were passaged as single cells using Accutase (Thermofisher). 5 µM ROCK inhibitor should be supplemented into media on the day of passage and withdrawn 24 hr post replating. NPCs should not be maintained for more than 10 passages.

extract_protocol:
Collected NPC samples were processed with 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 according to the manufacturer’s instructions.
Sequencing of the prepared library was performed on an Illumina sequencer generating approximately 450M reads in total.

treatment_protocol: To prepare dCas9-stable NPC lines, NPCs were single-cell seeded onto Geltrex-coated 6-w plates at 150,000 cells per cm2 in Neural Expansion Media containing dCas9-KRAB-Blast lentivirus. At the day of transduction, 0.1 ml of virus-containing medium was added into each well containing 2 ml of neural maintenance media. 24hr post-transduction, fed cells with fresh media containing 15 µg/ml blasticidin. Blasticidin was included in media through the experiment to prevent silence of the dCas9-KRAB-Blast, and the selection media was replaced daily for the first 72 hr of and subsequently every 48 hr for the growth and expansion of NPC. The transduction of dCas9-KRAB-expressing NPCs was performed as followed. One day before transduction, the dCas9-KRAB-expressing NSCs were seeded onto Geltrex-coated 6-well plates at a density of 2x10e5 cells per cm2. At the day of transduction, the media was further replaced once, and 50 µl of virus-containing medium was added into each well of the 24-well plates for transduction. 24 hr post induction, the virus-containing media were replaced with fresh media. Drug selection was performed by replacing the culture media containing 1 µg/µl of puromycin 48 hr post induction. The NSCs were allowed to grow for a further 72 hr before harvesting, with culture media replaced fresh daily. Survived cells were harvested using Accutase and frozen in Neural Expansion Media with 10% DMSO.

value: iPS-derived Neural Progenitor Cell

tag: cell line(s)


title: LNCaP: C_E2


title: SCN AncBE4max mouse embryo#3


title: hA3A(W98Y)-dCas12a-BE:S6, S4, DYR, CDK rep b


title: SCN AncBE4max mouse embryo#2


title: dCas9-KRAB_nosg_rep2

value: dCas9 only


title: SCN AncBE4max mouse embryo#1


title: CRISPRi-scRNA-Seq (NPC_05_07)

description: barcoded mRNA


title: hA3A(W98A)-dCas12a-BE:S6, S4, DYR, CDK rep b


title: SCN BE3 mouse embryo#16


title: hA3A-dCas12a-BE: CDK rep h; DYR rep d; S4 rep e; S6 rep c

value: hA3A-dCas12a-BE and hA3A-dCas12a-BE and hA3A-dCas12a-BE and hA3A-dCas12a-BE


title: SCN BE3 mouse embryo#15


title: VPS_NSC_H12_USR17005268L

data_processing:
ATAC-Seq data: All raw sequence reads generated by Illumina HiSeq 2000 have been de-complexed at the University of Minnesota Genomic Center and provided as 2x50 bp pair-end fastq files (100 M reads per sample). Adapter remnants, low-quality reads, and low QSEQ short sequences near either end of reads were processed by Trimmomatic (ILLUMINACLIP:NexteraPE-PE.fa:2:30:7, SLIDINGWINDOW:3:18, MINLENGTH:26). The survived sequences were separated into pair-end and single-end fastq files per sample, respectively. The pair-end and single-end fastq files were individually mapped against the human genome reference file including decoy sequences (GRCh38p7/hg38, 1000 Genome Project) using bowtie2 (-x 2000, -mm --qc-filter –met 1 –sensitive –no-mixed -t) and subsequently merged and sorted as BAM-formatted files using samtools, only uniquely mapped reads (MAPQ > 30) were collected. Picard tools MarkDuplicate was then used to remove all PCR and optical duplicated reads from the BAM file.
RNA-Seq data: RNA sequencing files were provided in the format of 2x150 bp pair-end (25 M reads per sample) fastq files. Briefly, libraries were prepared using the NEB Nextera kit with customised adapters. Since the sequencing facility had performed pre-cleaning on raw reads, no Trimmomatic action was performed. The files were subsequently mapped to the human hg38 genome (GRCh38p7) using STAR v 2.6.0 (--outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outSAMattrIHstart 0 --outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterIntronMotifs RemoveNoncanonical --outBAMcompression 10 --outBAMsortingThreadN 20 --outBAMsortingBinsN 20 --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --outSJfilterReads Unique --limitBAMsortRAM 10000000000 --alignSoftClipAtReferenceEnds No --quantTranscriptomeBAMcompression 10 10 ).
Genome_build: GRCh38.p7

source_name: Neural Progenitor Cell

extract_protocol:
At the day of harvesting the culture media was removed by aspiration and the cells were washed twice using 1 ml PBS each with aspiration. Subsequently, 600 µl of RLT Plus reagent was directly added into each well to homogenise cells in situ. Qiagen RNEasy plus kit was used for the extraction of total RNA according to the manufacturer’s protocol. Extracted RNAs were eluted into 50 µl of RNA-free water and the concentration was determined by nanodrop. Approximately 5 µg total RNA was recovered from each well.
Total RNAs isolated by using MirVana kit (Thermofisher) were used in RNA-seq. After QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Subsequently, terminal repair and sequencing adaptor ligation were applied to the templates. The double-stranded cDNA library is completed through size selection and PCR enrichment.
Reverse-transcription was performed using ThermoFisher High-capacity RNA-to-cDNA reverse transcription kit with random hexamers according to the manufacturer’s protocol. Briefly, 1 µg of total RNA was used for each 20 µl RT reaction. The reaction products were then diluted with 180 µl of RNase-free water for qPCR analysis. RNA quality control and gene expression quantification were performed by the qPCR method using gene-specific FAM-labelled TaqMan probes (ThermoFisher) against VPS45 with GAPDH as internal control on a Roche 480 II machine.


title: VPS_NSC_G7_USR17005270L


title: ExVivo_Blood_Death [SNS_134_expI]

value: Whole blood


title: hA3A(P134Y)-dCas12a-BE:S6, S4, DYR, CDK rep a


title: ExVivo_Blood_No_Death [REA1573_SS]

value: patient who will not die before 90 days


title: LNCaP: C_DMSO


title: hA3A(P134A)-dCas12a-BE:S6, S4, DYR, CDK rep a


title: SCN BE3 mouse embryo#12


title: VPS_NSC_B11_USR17005269L


title: VPS_NSC_A11_USR17005267L


title: SCN BE3 mouse embryo#11


title: hA3A(W104Y)-dCas12a-BE:S6, S4, DYR, CDK rep a


title: SCN BE3 mouse embryo#13


title: VPS_NSC_11_USR17005266L


title: hA3A(W104A)-dCas12a-BE:S6, DYR, CDK  rep a


title: hA3A(W98Y)-dCas12a-BE:S6, S4, DYR, CDK  rep a


title: SCN BE3 mouse embryo#10


title: NSC_21_USR17005244L


title: ExVivo_Blood_Death [SS_57exp2]


title: NSC_18_USR17005243L


title: ExVivo_Blood_Death [SS_93exp2]


title: ExVivo_Blood_Death [SNS_1_expI]


title: ExVivo_Blood_No_Death [SL_163expI]


title: SCN BE3 mouse embryo#14


title: hA3A(W98A)-dCas12a-BE:S6, S4, DYR, CDK rep a


title: SCN BE3 mouse embryo#9


title: NSC_16_USR17005242L


title: hA3A-dCas12a-BE: S4, CDK rep d and S6 rep b

value: hA3A-dCas12a-BE and hA3A-dCas12a-BE


title: SCN BE3 mouse embryo#8


title: 4-cell embryo_Ago2 kd_rep2 [RNA-seq]

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

institute: College of Life Science,Northeast Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 v2.1.0 with parameters -p 8 --dta -x -1 -2 -S
Fragments per kilobase of exon per million mapped fragments (FPKM) were calculated using StringTie. In short, exons from all isoforms of a gene were merged to create one meta-transcript.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: embryo blastomeres

growth_protocol: Embryos were collected from 7-week-old F1 superovulated female mice with 6.5 IU of pregnant mares’ serum gonadotropin (PMSG) and 5 IU human chorionic gonadotropin (hCG) 47 hours later, and crossed with F1 males. Embryos were isolated in M2 medium(Sigma) and cultured in KSOM medium at 37℃ in 5% CO2.

extract_protocol:
After the embryonic blastomere was treated with an acidic manipulation solution to remove the zona pellucida, we transferred it to the lysis solution for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR

value: embryo

value: embryo blastomeres


title: SCN BE3 mouse embryo#7

extract_protocol:
For DNA, after 72 hr, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre) or the cells were lysed in 2× SDS loading buffer for western blot.
For DNA, DNA-seq libraries were prepared with NEB Next Ultra™ II  FS DNA Library Prep Kit. Targeted deep sequencing was performed on Illumina Hiseq X ten or NextSeq 500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

value: mouse embryos


title: SCN BE3 mouse embryo#6


title: SCN BE3 mouse embryo#5


title: 4-cell embryo_Ago2 kd_rep1 [RNA-seq]


title: 4-cell embryo_control_rep2 [RNA-seq]

value: wild type


title: SCN BE3 mouse embryo#4


title: NT:VEG-b, VEG-a, TET, S6, S4, S3, RUN, RAG, RAG, PD1, FAN, DYR, DNM, CFT, CDK rep b

value: NT


title: NT:VEG-b, VEG-a, TET, S6, S4, S3, RUN, RAG, RAG, PD1, FAN, DYR, DNM, CFT rep c


title: NT:VEG-b, VEG-a, TET, S6, S4, S3, RUN, RAG, RAG, PD1, FAN, DYR, DNM, CFT, CDK rep a


title: hAID-dCas12a-BE:PD1, FAN, CDK rep c; VEG-a, TET, S3, RAG, RAG, DYR rep b

value: hAID-dCas12a-BE and hAID-dCas12a-BE


title: SCN BE3 mouse embryo#3


title: hAID-dCas12a-BE:VEG-b, VEG-a, TET, S4, S3, RAG, RAG, DYR, DNM rep c


title: ExVivo_Blood_Death [REA17264]

extract_protocol: Total RNA was extracted from blood samples using the PAX gene blood RNA System (Hombrechtikon, Switzerland). RNA was quantified by spectrometry (Nanodrop ND100, Nanodrop Technologies, Wilmington, Delaware). RNA was eluted with 80 µL of RNase-free H2O. RNA quality and concentration was measured by RNA Experion Bioanalyzer (BioRad, California USA) assay.

value: Female


title: NSC_12_USR17005241L

city: Evanston

address: 1001 University Place


title: ExVivo_Blood_No_Death [SNS_50_expI]


title: 2-cell embryo_Ago2 kd_rep2 [RNA-seq]


title: iPS_21_USR17005252L

source_name: iPS Cell


title: NSC_09_USR17005239L


title: NSC_08_USR17005238L


title: SCN BE3 mouse embryo#2


title: NSC_07_USR17005237L


title: SCN BE3 mouse embryo#1


title: 2-cell embryo_Ago2 kd_rep1 [RNA-seq]


title: NSC_11_USR17005240L


title: 2-cell embryo_control_rep2 [RNA-seq]


title: 4-cell embryo_control_rep1 [RNA-seq]


title: ExVivo_Blood_Death [SL_98expII]

value: Male


title: ExVivo_Blood_Death [SS_39esp2]

value: patient who will die before 90 days


title: ExVivo_Blood_No_Death [SIRS_25exp1]


title: iPS_16_USR17005250L

treatment_protocol: hiPSCs were cultured using feeder-free method on geltrex (Thermofisher)-coated plate in mTeSR1 media (StemCell). Media were changed daily and cells were passaged as single cells every 4-6 days using accutase (Thermofisher) in mTeSR1 in the presence of 5 mM ROCK inhibitor (R&D Systems)

value: iPS lines used to differentiate into all cell types


title: ExVivo_Blood_No_Death [SNS_46_expI]


title: iPS_18_USR17005251L

treatment_protocol: NPC are prepared using PSC Neural Induction Medium (Thermofisher) following vendor’s protocol with modification. Briefly, hiPSCs were replated as clumps in mTeSR media (STEMCELL) supplemented with 5 µM ROCK inhibitor (R&D Systems) on Day 0. From Day 1 to Day 9, cells were treated in PSC Neural Induction Medium with routinely removal of differentiated non-neuron cells. PSC Neural Induction Medium was prepared as 490ml Neurobasal Medium (Thermofisher) and 10 ml Neural Induction Supplement (Thermofisher). On Day 10, P0 NPCs were ready for passaging. From P0 to P3, NPCs were passaged using Rosette Selection Reagent (STEMCELL) and expanded in Neural Expansion Medium. Neural Expansion Medium was prepared as 245 ml Neurobasal Medium, 245 ml Advanced DMEM⁄F-12 media (Thermofisher) and 10ml Neural Induction Supplement. From P4, NPCs were passaged as single cells using Accutase (Thermofisher). 5 µM ROCK inhibitor were supplemented into media on the day of passage and withdrawn 24 hr post replating.

value: iPS-derived Neural Progenitor Cell


title: hAID-dCas12a-BE:S4, RAG, PD1  rep a; VEG-b, S6, RUN, FAN, DNM, CFT, CDK rep b


title: SCN BEACON2 mouse embryo#15


title: 2-cell embryo_control_rep1 [RNA-seq]


title: ExVivo_Blood_No_Death [SS_100exp1]


title: hAID-dCas12a-BE:VEG-b, TET, S6, S3, RUN, RAG, FAN, DYR, DNM, CFT, CDK rep a


title: MII oocyte_control_rep2 [RNA-seq]


title: SCN, HSD BEACON2 mouse embryo#14


title: SCN, HSD BEACON2 mouse embryo#13


title: iPS_11_USR17005248L


title: hAID-dCas12a-BE:S4, PD1 rep b; S6, RUN, CFT rep c; VEG-a rep a

value: hAID-dCas12a-BE and hAID-dCas12a-BE and hAID-dCas12a-BE


title: iPS_12_USR17005249L


title: SCN, HSD BEACON2 mouse embryo#12


title: MII oocyte_control_rep1 [RNA-seq]


title: iPS_08_USR17005246L


title: hA3B-dCas12a-BE:VEG-b, VEG-a, TET, S4, S3, RAG, RAG, FAN, DYR, DNM rep c


title: SCN, HSD BEACON2 mouse embryo#11


title: GFE5-Csf1r-mutant.2

data_processing:
Sequencing and base-calling was performed on the IlIllumina Novaseq 6000
Paired-end reads were aligned to the GRCz11.94 danio rerio genome using  STAR version 2.5.4b software. Annotations Danio_rerio.GRCz11.94.gtf were obtained from ftp.Ensembl.org
Gene level counts were obtained using HTSeq-count version 0.11.0
Differential gene expression analysis: EdgeR (Bioconductor). GSEA: GAGE (Bioconductor)
Genome_build: GRCz11.94
Supplementary_files_format_and_content: CPM values [.csv] semicolon-delimited files

source_name: skin mpeg1.1-GFP+ cells

growth_protocol: Standard adult zebrafish rearing conditions in multilink system at  26° C, with 12:12 h ligt/dark cycle

extract_protocol:
RNA isolation from FACS-sorted cells was perfored using the miRneasy Micro Kit (Qiagen) following manufacturer's instruction
Indexed cDNA libraries were obtained using the Ovation SoLo RNA-seq System (NuGen-TECAN) with the SoLo AnyDeplete probe mix

tag: developmental stage

value: adult 3mo

value: csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 tg(mpeg1-EGFP); tg(Kdrl:Cre); tg(act2b:loxP-STOP-loxP-DsRedexpress)

value: untreated


title: iPS_07_USR17005245L


title: hA3B-dCas12a-BE:S4, RAG, PD1, FAN rep a; VEG-b, S6, RUN, DNM, CFT, CDK rep b

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 GRCh38/hg38 human or GRCm38/mm10 mouse reference genome using BWA-MEM 0.7.9a.
Genome_build: hg38 for human samples and mm10 for mouse samples
Supplementary_files_format_and_content: Excel for Indels and Base Subtitutions

value: hA3B-dCas12a-BE and hA3B-dCas12a-BE


title: SCN, HSD BEACON2 mouse embryo#9


title: GFE4-B-Switch.1

source_name: skin mpeg1.1-GFP+;  act2b:loxP-STOP-loxP-DsRedexpress+ cells

value: wild-type tg(mpeg1-EGFP); tg(Kdrl:Cre); tg(act2b:loxP-STOP-loxP-DsRedexpress)


title: GFE3-B-Switch.3


title: GA_18_USR17005256L

source_name: GABergic , day-28 post induction

treatment_protocol: To prepare GABAergic neurons, NPCs were single-cell seeded in Virus-Neural Expansion Medium Cocktail onto laminin-coated (Sigma) plate at 200,000 cells per cm2 on Day 0. Virus-Neural Expansion Medium Cocktail was prepared as 7 ml Neural Expansion Media, 1 ml rtTA virus, 1 ml Ascl1-puro virus, 1 ml Dlx2-hygro virus and 5 µM ROCK inhibitor. On day 1, virus  were withdrawn and cells were fed with fresh Neural Expansion Media supplemented with 2µg/ml doxycycline (Sigma). From Day 2 to Day 6, cells were treated in Neural Expansion Media supplemented with 2 µg/ml doxycycline, 2 µg/ml puromycin (Thermofisher) and 100 µg/ml hygromycin (Thermofisher) to remove non-transduced cells. On day 7, switched media to conditioned NeuralbasalPlus Media and change media every 3 days. NeuralbasalPlus Media was conditioned using rat astrocyte (Thermofisher) 24 hr before media changing and BDNF, GDNF, NT-3. Doxycycline was withdrawn on Day 16 and 50 nM Ara-C was included in media if non-neuron cells were observed. On Day 28, neurons were harvested using Accutase for ATAC-seq or RNA isolation.

value: iPS-derived GABAergic Neurons, 28 days post induction


title: SCN, HSD BEACON2 mouse embryo#10


title: GA_21_USR17005257L


title: iPS_09_USR17005247L


title: hA3A-dCas12a-BE:PD1, CDK  rep c; RUN rep g; S6, DNM rep e; VEG-a, TET, S3, RAG, RAG, FAN rep b

source_name: HEK293T cells

value: hA3A-dCas12a-BE and hA3A-dCas12a-BE and hA3A-dCas12a-BE and hA3A-dCas12a-BE


title: hA3B-dCas12a-BE:PD1, CDK  rep c; VEG-a, TET, S3, RAG, RAG, FAN, DYR rep b


title: GFE2-WT.2


title: hA3A-dCas12a-BE:RUN rep h; S6, CDK rep f; VEG-b, VEG-a, TET, S4, S3, RAG, RAG, FAN, DYR, DNM rep c

value: hA3A-dCas12a-BE and hA3A-dCas12a-BE and hA3A-dCas12a-BE


title: GFE6-Csf1r-mutant.3

value: csf1raj4e1/j4e1; csf1rbsa1503/csf1rbsa1503 (mpeg1-EGFP); (Kdrl:Cre); (act2b:loxP-STOP-loxP-DsRedexpress)


title: GFE1-WT.1


title: hA3A-dCas12a-BE:DNM rep d; RUN, CFT rep c; S4, PD1, CDK rep b; VEG-a, S6 rep a


title: SCN, HSD BEACON2 mouse embryo#8

value: mouse embryos


title: GA_08_USR17005253L


title: GA_09_USR17005254L


title: hA3B-dCas12a-BE:VEG-b, TET, S6, S3, RUN, RAG, DYR, DNM, CFT, CDK rep a


title: hA3B-dCas12a-BE:S4, PD1  rep b; S6, RUN, CFT rep c and VEG-a rep a

value: hA3B-dCas12a-BE and hA3B-dCas12a-BE and hA3B-dCas12a-BE


title: SCN, HSD BEACON2 mouse embryo#5


title: ESC_rep3_ATACseq

city: Fort Collins

first: Michelle

middle: M

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

data_processing:
Raw sequencing reads were trimmed with Trim_Galore, a wrapper around Cutadapt (v0.4.0), to remove residual Illumina adapter sequences and low quality (q<20) ends, keeping unpaired reads and reads 10 bp or longer after trimming.
Trimmed reads were aligned to the genome using BWA (v0.7.17) aln (-q 15) and sampe.
PCR duplicates were removed with PicardTools (v2.8.1), and mitochondrial and low-quality alignments. (q<15) were removed with SAMtools (v1.7)
Processed alignments were converted to bigwig format using bamCoverage from the DeepTools suite, which binned the genome into 50 bp windows and calculated normalized signal (reads per kilobase million; RPKM) in each window.
Broad peaks were called with MACS2 (v2.1.1), using a q-value cutoff of 0.05, and settings --nomodel --shift -100 --extsize 200.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Bigwig files show genome-wide normalized ATAC-seq signal; BED files show regions of ATAC-seq enrichment (peaks).

organism: Bos taurus

source_name: Embryonic stem cells

growth_protocol: Follicles measuring 2-10 mm were aspirated to obtain cumulus oocyte complexes (COCs). Only COCs with healthy layers of cumulus cells were selected for maturation. These were washed in collection medium (6:4 M199 (Sigma M7653)): SOF-Hepes, supplemented with 2% fetal bovine serum (FBS; Hyclone/Thermo Scientific) and transferred to maturation medium (modified M199 medium (Sigma M2154)) supplemented with ALA-glutamine (0.1 mM), sodium pyruvate (0.2 mM), gentamicin (5 μg/ml), EGF (50 ng/ml), oFSH (50 ng/ml), bLH (3 μg/ml), cysteamine (0.1 mM), and 10% FBS. After COCs matured for 24 h, MII oocytes were washed in SOF-IVF medium (107.7 mM NaCl, 7.16 mM KCl, 1.19 mM KH2PO4, 0.49 mM, MgCl2, 1.17 mM CaCl2, 5.3 mM sodium lactate, 25.07 mM NaHCO3, 0.20 mM sodium pyruvate, 0.5 mM fructose, 1X non-essential amino acids, 5 μg/ml gentamicin, 10 μg/ml heparin, 6 mg/ml fatty acid-free (FFA) BSA) and transferred to drops of SOF-IVF medium under mineral oil. Frozen semen from a Holstein bull was thawed, and 106 sperm/ml were added to drops with MII oocytes, which were incubated at 38.5°C for 12-18 h. Zygotes were then removed from fertilization medium, and cumulus cells were removed by vortexing for 5 min in SOF-Hepes medium. Zygotes were then transferred to culture medium (KSOMaa supplemented with 4mg/mL BSA) under mineral oil, and incubated at 38.5°C in 5% CO2, 5% O2, and 90% N2. On day three, the culture medium was supplemented with 5% stem-cell qualified FBS (Gemini Bio 100-525). Blastocyst development was evaluated at 7 days post-insemination (dpi). CTFR-bESC lines (Bogliotti et al, 2018) were cultured in CTFR medium consisting in custom mTeSR1 (devoid of TGFb and FGF2) supplemented with 20 ng/mL human FGF2 (100-18B, Peprotech), 2.5 μM IWR-1 (I0161, Sigma Aldrich), and 100 U/mL penicillin - 100 μg/mL streptomycin (15140-122, Gibco) on irradiated mouse embryonic fibroblast (MEF) (A34180, Gibco) at 37°C and 5% CO2. Cells were sub-cultured every 4-5 days at 1:10 split ratio using TrypLE Express (12604-013, Gibco). Culture medium was changed daily between passages. To increase cell survival, bESC culture medium was supplemented with 10 μM ROCK inhibitor Y-27632 (ALX-270-333-M005, Enzo) at seeding.

extract_protocol:
Pools of oocytes and embryos were collected for ATAC-seq library preparation from three separate collections per developmental stage. Embryos intended for collection at the 2-cell, 4-cell, or 8-cell stages were divided into two groups, one of which was supplemented with α-amanitin, and cultured simultaneously. Germinal vesicle-stage oocytes were collected for ATAC-seq prior to maturation. Preimplantation embryos were collected at the 2-cell (30-32 h post-insemination), 4-cell (2 dpi), 8-cell (3 dpi), and morula stages (5 dpi). Oocytes or embryos (a minimum of 500 cells) were treated with pronase (10 mg/ml) to completely remove the zona pellucida and washed with SOF-Hepes on a warming plate. Cells were then transferred to 1 ml cold SOF-Hepes, and centrifuged at 500 rcf, 4°C, for 5 min. Morulae were subjected to additional vortexing for 3 min in cold ATAC-seq lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Cell pellets were then resuspended in 1 ml cold ATAC-seq cell lysis buffer and centrifuged at 500 rcf, 4°C, for 10 min, and supernatant was aspirated to isolate nuclear pellets, prior to library preparation.To isolate ICMs for ATAC-seq by immunosurgery, blastocysts were treated with pronase (10 mg/ml) and washed in SOF-Hepes medium, then washed in 20% anti-bovine whole serum (B8270-2ML SIGMA, dilute in SOF-Hepes medium), and transferred to individual drops of 20% anti-bovine whole serum solution under mineral oil (20 ul per drop). Blastocysts were incubated for 1 h at 38.5°C, washed in SOF-Hepes medium, then washed in 20% guinea pig complement (Innovative Grade US origin, IGP-COMPL-21249) and transferred to individual drops of 20% guinea pig complement solution under mineral oil (20 ul drop). Blastocysts were again incubated for 1 h at 38.5°C. ICM were isolated by pipetting, treated with trypsin for 2-3 min, and pipetted several times before adding 10% fetal bovine serum to stop trypsinization. ICM cells were then washed in 1 ml cold SOF-Hepes medium and centrifuged at 500 rcf, 4°C, for 5 min. Cell pellets were then resuspended in 1 ml cold ATAC-seq cell lysis buffer and centrifuged at 500 rcf, 4°C, for 10 min, and supernatant was aspirated to isolate nuclear pellets. Before cell lysis and library preparation, CTFR-bESCs were trypsinized and separated from MEF feeders by plating the cell suspension in CTFR culture medium supplemented with 10 μM ROCK inhibitor Y-27632 for 1 h in a 60 mm cell culture dish (430196, Corning) at 37°C and 5% CO2. After incubation, cells that did not adhere to the culture dish were recovered for downstream processing. For each library, 50,000 ESC were aliquoted and centrifuged at 500 rcf, 4°C, for 5 min, then washed with 50 ul cold 1xPBS buffer, then centrifuged at 500 rcf, 4°C, for 5 min, then resuspended in 50 ul cold ATAC-seq cell lysis buffer, then centrifuged at 500 rcf, 4°C, for 10 min to isolate nuclear pellets.
Nuclear pellets were resuspended in 50 μl transposition reaction mix (25 μl TD buffer (Nextera DNA Library Prep Kit, Illumina), 2.5 μl TDE1 enzyme (Nextera DNA Library Prep Kit, Illumina), 22.5 μl nuclease-free H2O) and incubated for 60 min at 37°C, shaking at 300 rpm. Transposed DNA was purified with the MinElute PCR purification kit (Qiagen, Hilden, Germany) and eluted in 10 μl buffer EB. Libraries were then PCR amplified. 50 μl reactions (25 μl SsoFast Evagreen supermix with low ROX (Bio-Rad, Hercules, CA), 0.6 μl 25 μM custom Nextera PCR primer 1, 0.6 μl 25 μM custom Nextera PCR primer 2 (for a list of primers, see Buenrostro et al (2015)), 13 μl nuclease-free H2O, and 10 μl eluted DNA) were cycled as follows: (1) 72°C for 5 min, 98°C for 30 s, then (2) thermocycled at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. Libraries from GV oocytes, 2-cell, and 4-cell embryos were thermocycled for 13 cycles, and 8-cell and morulae libraries were thermocycled for 11 cycles. PCR-amplified libraries were again purified with the MinElute PCR purification kit and eluted in 10 μl buffer EB. The sub-nucleosomal length fraction of each library (150-250 bp) was size selected using the PippinHT system (Sage Science, Beverly, MA) with 3% agarose cassettes.

treatment_protocol: If embryos were to be transcriptionally inhibited, the culture medium was supplemented with α-amanitin (50 μg/ml) on day one.

value: ESC

value: Control


title: ESC_rep1_ATACseq


title: ESC_rep2_ATACseq


title: GA_07_USR18003081L


title: GA_16_USR17005255L


title: SCN, HSD BEACON2 mouse embryo#7


title: rA1-dCas12a-BE:VEG-b, VEG-a, TET, S4, S3, RAG, RAG, FAN, DYR, DNM  rep c


title: hA3A-dCas12a-BE:CDK  rep e; S4, RAG, PD1, FAN rep a; S6 rep d; VEG-b, RUN, DYR, DNM, CFT rep b


title: hA3A-dCas12a-BE: VEG-b, TET, S3, RUN, RAG, DYR, DNM, CFT, CDK  rep a


title: SCN, HSD BEACON2 mouse embryo#2


title: ICM_rep3_ATACseq

source_name: In vitro produced embryo

value: ICM


title: SCN, HSD BEACON2 mouse embryo#6