title: SNP normalization_Normal blood #Female

status: Public on Nov 01 2020

city: KOLKATA

first: CHINMAY

middle: KUMAR

last: PANDA

state: WEST BENGAL

address: 37, SP MUKHERJEE ROAD, KOLKATA

department: ONCOGENE REGULATION UNIT

country: India

institute: CHITTARANJAN NATIONAL CANCER INSTITUTE, INDIA

hyb_protocol: Equal amount of labeled Test & Control DNA sample was added into a fresh tube containing 25 µl of Human Cot-1 DNA (1mg/ml),  26ul of Agilent 10X blocking agent and 130ul Agilent 2X hybridization buffer. The total hybridization volume was 45ul. The above hybridization mix was denatured at 95°C for 3 minutes and incubated the microfuge tubes at 37°C for 30 minutes.  The samples were hybridized at 65°C for 40 hours in the hybridization chamber. After hybridization, the slides were washed using aCGH Wash Buffer1 (Agilent Technologies, Part Number 5188-5221) at room temperature for 5 minutes and aCGH Wash Buffer 2 (Agilent Technologies, Part Number 5188-5222) at 37°C for 1 minutes. The slides were then washed with Acetonitrile for 10 seconds.

scan_protocol: Agilent Scanner (Agilent Technologies, Part Number G2565CA).

data_processing: Images were quantified using Agilent Feature Extraction Software. Feature extracted raw data was normalized using Lowes normalization and analyzed Agilent CytoGenomics 2.9 Software.

source_name: Coriell - NA12878 Female

label_protocol: Agilent Direct method has been used for the sample processing. About 1000 ng of control and test DNA was used for the restriction digestion in the master mix containing AluI and RsaI restriction enzymes as per manufactures recommendation. The samples were incubated at 37°C for 2 hours followed by heat inactivation of enzymes at 65°C for 20 minutes. To confirm the efficiency of restriction enzymes to obtain fragments of size 200-500bp, about 2 μL of the digested gDNA was tested on a 0.8% agarose gel. Labeling of samples was done by random priming method, in which the random hexamers, Cy3-dUTP & Cy5-dUTP, dNTP, Buffer and Klenow enzyme was used. Briefly, 1X Random primer mix was added to each of 26µl digested control and test samples. The DNA was denatured at 95 °C for 3 minutes followed by snap chill on ice for 5 minutes. Master mix for Cy3 and Cy5 dNTPs was done separately to ensure that,  the  control sample is labeled with Cy3 and test sample with Cy5 respectively. About 19 ul of labeling master mix prepared as per manufacturers recommendation was added to the denatured control and test DNA sample and incubated at 37°C for 2 hours followed by enzyme heat inactivation at 65°C for 10 minutes. The labeled samples were cleaned up by Amicon 30kDa filter size exclusion filter.

extract_protocol: DNA isolation from peripheral blood lymphocytes (N) and cancer tissues (T),   using standrad Phenol/ Chloroform method. Tumor tissue were microdissected   for tumor cell enrichment before DNA extraction.

treatment_protocol: tumor tissues vs normal peripheral blood lymphocytes

value: Coriell - NA12878 Female

tag: age

tag: Stage

tag: grade

tag: smoking history

tag: alcohol ingestion

tag: drinking water source

value: F

tag: arsenic in tumor tissue

tag: occupation of the subject

source_name: Peripheral Blood lymphocytes

value: housewife

tag: reference

value: matched normal blood


title: 18537

status: Public on Oct 05 2020

type: genomic

city: Boston

first: Sunita

middle: R

last: Setlur

address: 221 Longwood Avenue

country: USA

institute: Brigham and Women's Hospital

description: Normal EBV transformed lymphoblastoid cell line DNA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: LCL

label_protocol: Samples were labeled according to the standard Illumina protocol

extract_protocol: Genomic DNA was purchased from Coriell Cell Repository

tag: gender

value: Female

tag: cell type

value: Lymphoblastoid cell lines

tag: disease state

value: Normal


title: 18562

value: Male


title: 12892


title: 18956


title: 18872


title: H3K4me3-20-8

status: Public on Sep 22 2020

type: SRA

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

library_source: genomic

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed reads were aligned using bowtie 1.1.2
Reads were extended to 250bp
Sample was normalized and input subtracted
Sample was converted to BigWig format
Genome_build: hg19
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format

source_name: GM12878 cell line

growth_protocol: GM12878 was bought from Coriell Institute for Medical Research. Cells were cultured in RPMI 1640 media (30-2001, ATCC) supplemented with 15% FBS (16000044, Life Technologies Corporation), 100U/mL Penicillin-Streptomycin (15140122, Life Technologies Corporation) in an incubator maintaining 5% CO2 and 37 ℃. Mycoplasma contamination was tested every 6 months using Universal Mycoplasma Detection Kit (ATCC® 30-1012K™).

extract_protocol:
Cells were suspended in 10 µl PBS and mixed with 10 µl lysis buffer [4% Triton X-100, 100 mM Tris (pH 7.5), 100 mM NaCl, and 30 mM MgCl2] containing freshly added 1% PIC (0.1 µl) and 1 mM PMSF (0.1 µl of 100mM). After 10-min incubation at room temperature, 0.21 µl of 500 m0.1M CaCl2 and 0.2 µl of 100U/µl MNase were added followed by another 10-min incubation. The reaction wais stopped by adding 0.2.22 µl of 0.5M EDTA , and incubated on ice for 10 min. Samples containing more than 1,000 cells was centrifuged at 16,100 g at 4 ℃ for 5min, and supernatant was transferred to a new Eppendorf tube. Chromatin solution can be stored on ice for a few hours.
Adapters were added by tagmentation followed by PCR amplification. The use of microfluidic device and associated procedures are detailed in our paper.

tag: number of cells

tag: cell line

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: 12056


title: H3K4me3-20-7


title: 19238


title: 12889


title: 19239


title: 18555


title: 12877


title: 18552


title: H3K4me3-20-5


title: H3K4me3-20-6


title: 18561


title: 18517


title: 18871


title: 10851


title: 18547


title: SNP normalization_Normal blood #Male

source_name: Coriell- NA12891 Male

value: Coriell- NA12891 Male

value: M

value: farmer


title: 12878


title: 18870


title: H3K4me3-20-4


title: 12891


title: H3K4me3-20-3


title: H3K4me3-20-2


title: H3K4me3-40-7


title: H3K4me3-40-8


title: H3K4me3-40-1


title: H3K4me3-40-4


title: H3K4me3-100-6


title: H3K4me3-40-3


title: H3K4me3-100-8


title: H3K4me3-100-7


title: H3K4me3-40-5


title: H3K4me3-100-1


title: H3K4me3-40-6


title: H3K4me3-100-4


title: IAV/PR8-infected HEK293T with IFI16-Flag overexpression

status: Public on Sep 17 2020

city: Bei jing

first: zhimin

last: jiang

address: No.2 Yuanmingyuan West Road, Haidian District, Beijing

department: college of Veterinary medicine

country: China

institute: China agriculture university

library_source: transcriptomic

data_processing:
callpeak/mapping/meme
Genome_build: PR8/H1N1 genome
Supplementary_files_format_and_content: callpeak/mapping/meme

molecule: total RNA

organism:
Homo sapiens
Influenza A virus

source_name: RIG-I knockout 293T cells

extract_protocol:
1 mL Tri-reagent (Sigma) was added to each sample, and RNA was harvested according to the manufacturer’s instructions. RNA was eluted from beads and examined by  RNA-seq
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: HEK293T cells were transfected with FLAG-tagged RIG-I or IFI16 constructs and infected with PR8 (MOI = 2) for 12 hr. Cells were disrupted in IP lysis buffer(25U RNasin) and lysates were then incubated with 30 mL/sample anti-FLAG agarose bead overnight with rotation at 4 C. Beads were collected by centrifugation, washed ten times with NT2 buffer.resuspended in 250 mL of DNase digestion buffer (40 mM Tris  [pH 8.0], 10 mM MgSO4, 1 mM CaCl2), and treated with 25U RNasin (Promega) and 2U DNase I (NEB) at 37 C for 20 min. Beads were then washed and resuspended in 100 mL NT2 buffer and treated with 4 units proteinase K at 55 C for 30 min. ( as described in the Thapa et al., 2016, Cell Host & Microbe 20, 674–681).

tag: iav strain

tag: molecule subtype

value: Viral RNA


title: H3K4me3-40-2


title: H3K4me3-100-3


title: H3K4me3-100-2


title: IAV/PR8-infected HEK293T with RIG-I-Flag overexpression


title: FX_FMRP_ChIP

status: Public on Sep 13 2020

city: Syracuse

first: Wenyi

last: Feng

state: NY

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

description:
Chromatin Immunoprecipitated DNA
MACS_AC090814B_to_A_peaks.bed (MACS peak calling)

data_processing:
[MACS_AC090814B_to_A_peaks.bed and updown.bed] alignment by Bowtie2, peak-calling by MACS2.  Quantitative threshold in MACS2: P< 1E-05.
[all other files]  alignment by Bowtie2, merging BAM files from multiple sequencing of the same sample (e.g. EH040213B*.fastq.gz, EH040213B2*.fastq.gz, and EH040213B3*.fastq.gz are three sequence files associated with the sample EH040213B), peak-calling by MACS2, followed by consensus peak (among replicate experiments) identification by DiffBind.  Quantitative threshold in MACS2: P< 1E-05.
Genome_build: hg19
Supplementary_files_format_and_content: MACS peak calling

source_name: EBV-transformed lymphoblasts from FX individual

growth_protocol:
EBV transformed lymphocytes derived from a normal individual(GM06990) and a Fragile X individual (GM03200) were grown in RPMI1640, supplemented with GlutaMAX, 15% heat-inactivated FBS, 100 IU/ml penicillin and 100 μg/ml streptomycin, to a density of 0.4-0.5x10E6 cells/ml.
EBV transformed lymphocytes derived from a normal individual(GM06990) and a Fragile X individual (GM03200) were grown in RPMI1640, supplemented with GlutaMAX, 15% heat-inactivated FBS, 100 IU/ml penicillin and 100 ug/ml streptomycin.

extract_protocol:
Cells were thawed on ice with 1 ml Farham's lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, Halt protease inhibitor cocktail (Thermo Scientific)) for 5 m.  Nuclei were prepared by centrifuging the lysate at 2000 rpm for 5 m.  The nuclear pellet was resuspended in 300 μl RIPA (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Halt protease inhibitor cocktail).  Samples were sonicated in a Bioruptor (Diagenode) at high setting for a total time of 40 m with 30 s ON and 30 s OFF at 4°C.  The sonicated mixture was centrifuged at 13,500 rpm for 15 m at 4°C and the volume of supernatant was adjusted to 1 ml with RIPA buffer.  100 μl of this mixture was set aside as "input" and the remaining nuclear fraction was used for immunoprecipitation.  Both aliquots were snap frozen in liquid nitrogen and stored at -80°C until ready for immunoprecipation.  10 μg of monoclonal anti-FMRP antibody (Covance, now Biolegend, Cat#MMS-5231) was conjugate with M280 Dynabeads sheep anti-mouse IgG (Life Technologies).  The thriced washed beads (with PBS/BSA) were incubated with 900 μl sonicated nuclear fraction overnight at 4°C with agitation.  The beads were then washed 5 times with cold LiCl wash buffer (100 mM Tris pH7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate), followed by a single wash in TE (10 mM Tris-HCl pH7.5, 0.1 mM EDTA). The immunoprecipitates were eluted with 200 μl of IP elution buffer (1% SDS, 0.1 M NaHCO3) at 65°C for 2 h with vortexing every 30 m.  The 100 μl "input" was thawed and together with the eluted immunoprecipitates were reverse-crosslinked at 65°C overnight.  The samples were then used for ChIP-seq library construction.
DNA was purified from all samples (input and immunoprecipitates) using Qiagen PCR clean-up kit and then end-repaired in a 100 μl reaction (1x End-repair buffer, 250 μM dNTP mix, 1 mM ATP, and 3 μl End-It Enzyme (Epicentre)) for 45 m at room temperature.  Labeled DNA was purified using Qiagen PCR clean-up kit, A-tailed using Klenow(exo-) (NEB E6055A), purified again with Qiagen PCR clean-up kit, and ligated to Ilumina adaptors using standard conditions.  Ligated DNA was purified with Qiagen PCR clean-up kit and amplified by PCR (18 cycles) using index primers (98°C, 5m; 18 cycles of 98°C, 20s; 65°C, 15s; 72°C, 1m; followed by 1 cycle of 72°C, 5m).  The PCR products were purified by AmPure beads (AgenCourt) to rmove free adaptors.
10E6 PBS-washed cells were embedded in 0.5% Incert low-melting point agarose in PBS and cast into plugs (0.5cmx1cmx1.5mm).  Plugs were then incubated in  6 ml lysis buffer (0.5M EDTA, 1% Sarkosyl, 200ug/ml Proteinase K) at 50 degree celcius for 48 h, with a buffer exchange at 24 h.  Plugs were then washed three times, for 1 h each, with 6 ml TE at room temperature.
The DNA in TE-washed agarose plugs was then in-gel end-labeled with biotinylated dNTP mix (1 mM dTTP, dCTP, dGTP, 0.84 mM dATP, 0.16 mM Biotin-14-dATP) using End-It Kit (Epicentre). Plugs were then treated with beta-Agarase (NEB) to digest agarose and release DNA. DNA sample was then sonicated using a Covaris M220 using the snap-cap DNA 300bp shearing protocol.  DNA was then processed using a PCR Cleanup Kit (Qiagen) and run on agarose gel to verify the fragmentation pattern of DNA and quantified on a Nanodrop. 10-11 microgram of DNA was then end-repaired using a regular End-It kit and purified by the PCR Clean-up Kit.  The DNA was then A-tailed by A-tail Kit or exo-Klenow (NEB) and purified by PCR Clean-up kit, followed by quantification on a Nanodrop.  M270 Dynabeads (Life Technologies) were used to purify biotinylated DNA.  DNA bound to beads was calculated by measuring the quantity of DNA in the flow through.  DNA-bound beads were then resuspended in a T4-ligase mix containing Illumina adaptors.  400 ng of DNA bound to beads was used for PCR amplification using KAPA Hotstart Ready Mix (KAPA).  Each sample was given a specific index primer for multiplexing.  PCR product was then run on agarose gel to verify amplification and quantity.  AMPure beads (Agencourt) were used to remove free adaptors and the final product was analyzed on agarose gel. Break-seq libraries were sequenced on Illumina HiSeq 2500 with 100 or 150 bp paired-end reads, followed by Break-seq data analysis.

treatment_protocol:
ChIP-seq procedures based on Richard Myers lab protocol.  Cells were fixed with 1% formaldehyde for 10 m at room temperature and then blocked with 0.125 M glycine.  Cells were washed twice with cold PBS and then collected at 2x10E7 cells per ChIP reaction, snap frozen in liquid nitrogen and stored at -80°C until further use.
At a density of 0.4-0.5x10E6 cells/ml, cells were treated with solvent (DMSO, 0.02%), 0.03 micromolar aphidicolin (APH), 0.3 micromolar APH, or nothing at all.  APH was dissolved in 0.02% DMSO at both concentrations.  After 24 h treatment, cells were harvested for Break-seq analysis.

tag: treatment

value: Untreated

tag: biological replicate no.

tag: technical replicate no.


title: NM_WC

description:
Whole genomic DNA
DNA-seq; note the "input" control from the ChIP protocol described above was used to construct a whole genome DNA library with identical procedures as the immunoprecipitated DNA.
All processed files concerning GM06990 (MACS peak calling (as control for Break-seq samples))

data_processing:
Library strategy: DNA-seq
[MACS_AC090814B_to_A_peaks.bed and updown.bed] alignment by Bowtie2, peak-calling by MACS2.  Quantitative threshold in MACS2: P< 1E-05.
[all other files]  alignment by Bowtie2, merging BAM files from multiple sequencing of the same sample (e.g. EH040213B*.fastq.gz, EH040213B2*.fastq.gz, and EH040213B3*.fastq.gz are three sequence files associated with the sample EH040213B), peak-calling by MACS2, followed by consensus peak (among replicate experiments) identification by DiffBind.  Quantitative threshold in MACS2: P< 1E-05.
Genome_build: hg19
Supplementary_files_format_and_content: MACS peak calling

source_name: EBV-transformed lymphoblasts from normal individual


title: FX_WC

description:
Whole genomic DNA
DNA-seq; note the "input" control from the ChIP protocol described above was used to construct a whole genome DNA library with identical procedures as the immunoprecipitated DNA.
All processed files concerning GM03200 (MACS peak calling (as control for Break-seq samples))


title: FX_003aph_PacI_digested

description:
Labeled DNA double strand breaks
WF040213F.vs.Input_FX_peaks.xls.pval_e-5.10updown.narrowPeak (MACS peak calling)

data_processing:
Library strategy: Break-seq
[MACS_AC090814B_to_A_peaks.bed and updown.bed] alignment by Bowtie2, peak-calling by MACS2.  Quantitative threshold in MACS2: P< 1E-05.
[all other files]  alignment by Bowtie2, merging BAM files from multiple sequencing of the same sample (e.g. EH040213B*.fastq.gz, EH040213B2*.fastq.gz, and EH040213B3*.fastq.gz are three sequence files associated with the sample EH040213B), peak-calling by MACS2, followed by consensus peak (among replicate experiments) identification by DiffBind.  Quantitative threshold in MACS2: P< 1E-05.
Genome_build: hg19
Supplementary_files_format_and_content: MACS peak calling

growth_protocol:
EBV transformed lymphocytes derived from a normal individual(GM06990) and a Fragile X individual (GM03200) were grown in RPMI1640, supplemented with GlutaMAX, 15% heat-inactivated FBS, 100 IU/ml penicillin and 100 μg/ml streptomycin.
EBV transformed lymphocytes derived from a normal individual(GM06990) and a Fragile X individual (GM03200) were grown in RPMI1640, supplemented with GlutaMAX, 15% heat-inactivated FBS, 100 IU/ml penicillin and 100 ug/ml streptomycin.

extract_protocol:
10E6 PBS-washed cells were embedded in 0.5% Incert low-melting point agarose in PBS and cast into plugs (0.5cmx1cmx1.5mm).  Plugs were then incubated in  6 ml lysis buffer (0.5M EDTA, 1% Sarkosyl, 200ug/ml Proteinase K) at 50 degree celcius for 48 h, with a buffer exchange at 24 h.  Plugs were then washed three times, for 1 h each, with 6 ml TE at room temperature.
The DNA in TE-washed agarose plugs was then in-gel end-labeled with biotinylated dNTP mix (1 mM dTTP, dCTP, dGTP, 0.84 mM dATP, 0.16 mM Biotin-14-dATP) using End-It Kit (Epicentre). Plugs were then treated with beta-Agarase (NEB) to digest agarose and release DNA. DNA sample was then sonicated using a Covaris M220 using the snap-cap DNA 300bp shearing protocol.  DNA was then processed using a PCR Cleanup Kit (Qiagen) and run on agarose gel to verify the fragmentation pattern of DNA and quantified on a Nanodrop. 10-11 μg of DNA was then end-repaired using a regular End-It kit and purified by the PCR Clean-up Kit.  The DNA was then A-tailed by A-tail Kit or exo-Klenow (NEB) and purified by PCR Clean-up kit, followed by quantification on a Nanodrop.  M270 Dynabeads (Life Technologies) were used to purify biotinylated DNA.  DNA bound to beads was calculated by measuring the quantity of DNA in the flow through.  DNA-bound beads were then resuspended in a T4-ligase mix containing Illumina adaptors.  400 ng of DNA bound to beads was used for PCR amplification using KAPA Hotstart Ready Mix (KAPA).  Each sample was given a specific index primer for multiplexing.  PCR product was then run on agarose gel to verify amplification and quantity.  AMPure beads (Agencourt) were used to remove free adaptors and the final product was analyzed on agarose gel. Break-seq libraries were sequenced on Illumina Hi-Seq 2500 with 100 or 150 bp paired-end reads, followed by Break-seq data analysis.
10E6 PBS-washed cells were embedded in 0.5% Incert low-melting point agarose in PBS and cast into plugs (0.5cmx1cmx1.5mm).  Plugs were then incubated in  6 ml lysis buffer (0.5M EDTA, 1% Sarkosyl, 200ug/ml Proteinase K) at 50 degree celcius for 48 h, with a buffer exchange at 24 h.  Plugs were then washed three times, for 1 h each, with 6 ml TE at room temperature.
The DNA in TE-washed agarose plugs was then in-gel end-labeled with biotinylated dNTP mix (1 mM dTTP, dCTP, dGTP, 0.84 mM dATP, 0.16 mM Biotin-14-dATP) using End-It Kit (Epicentre). Plugs were then treated with beta-Agarase (NEB) to digest agarose and release DNA. DNA sample was then sonicated using a Covaris M220 using the snap-cap DNA 300bp shearing protocol.  DNA was then processed using a PCR Cleanup Kit (Qiagen) and run on agarose gel to verify the fragmentation pattern of DNA and quantified on a Nanodrop. 10-11 microgram of DNA was then end-repaired using a regular End-It kit and purified by the PCR Clean-up Kit.  The DNA was then A-tailed by A-tail Kit or exo-Klenow (NEB) and purified by PCR Clean-up kit, followed by quantification on a Nanodrop.  M270 Dynabeads (Life Technologies) were used to purify biotinylated DNA.  DNA bound to beads was calculated by measuring the quantity of DNA in the flow through.  DNA-bound beads were then resuspended in a T4-ligase mix containing Illumina adaptors.  400 ng of DNA bound to beads was used for PCR amplification using KAPA Hotstart Ready Mix (KAPA).  Each sample was given a specific index primer for multiplexing.  PCR product was then run on agarose gel to verify amplification and quantity.  AMPure beads (Agencourt) were used to remove free adaptors and the final product was analyzed on agarose gel. Break-seq libraries were sequenced on Illumina HiSeq 2500 with 100 or 150 bp paired-end reads, followed by Break-seq data analysis.

treatment_protocol:
At a density of 0.4-0.5x10E6 cells/ml, cells were treated with solvent (DMSO, 0.02%), 0.03 μM aphidicolin (APH), 0.3 μM APH, or nothing at all.  APH was dissolved in 0.02% DMSO at both concentrations.  After 24 h treatment, cells were harvested for Break-seq analysis.
At a density of 0.4-0.5x10E6 cells/ml, cells were treated with solvent (DMSO, 0.02%), 0.03 micromolar aphidicolin (APH), 0.3 micromolar APH, or nothing at all.  APH was dissolved in 0.02% DMSO at both concentrations.  After 24 h treatment, cells were harvested for Break-seq analysis.

value: 0.03 μM APH in 0.02% DMSO


title: NM_FMRP_ChIP

value: anti-FMRP antibody (Covance, now Biolegend, Cat#MMS-5231)


title: H3K4me3-20-1


title: FX_dmso_PacI_digested

description:
Labeled DNA double strand breaks
WF040213E.vs.Input_FX_peaks.xls.pval_e-5.10updown.narrowPeak (MACS peak calling)


title: SetE_NM_nt

description:
Labeled DNA double strand breaks
NM.NT.peaks.bed (MACS peak calling)


title: SetE_NM_dmso

description:
Labeled DNA double strand breaks
NM.DMSO.peaks.bed (MACS peak calling)


title: SetE_NM_03aph

description:
Labeled DNA double strand breaks
NM.APH.peaks.bed (MACS peak calling)

value: 0.3 μM APH in 0.02% DMSO


title: SetE_NM_003aph


title: SetE_FX_dmso

description:
Labeled DNA double strand breaks
FX.DMSO.peaks.bed (MACS peak calling)


title: SetD_NM_dmso


title: SetD_NM_nt


title: SetD_FX_nt

description:
Labeled DNA double strand breaks
FX.NT.peaks.bed (MACS peak calling)


title: H3K4me3-100-5


title: SetB_NM_dmso


title: SetD_NM_003aph


title: SetB_NM_003aph


title: SetD_FX_03aph

description:
Labeled DNA double strand breaks
FX.APH.peaks.bed (MACS peak calling)


title: SetA_FX_dmso


title: SetA_NM_dmso


title: SetB_FX_dmso


title: SetA_NM_003aph


title: SetD_FX_003aph


title: SetE_FX_003aph


title: SetA_FX_003aph


title: SetB_FX_003aph


title: GM12878 nuclei exp2 processed with SNARE-seq2 protocol (RNAseq)

status: Public on Sep 09 2020

city: La Jolla

first: Kun

last: Zhang

state: CA

address: 9500 Gilman Dr Mailcode: 0412

department: Bioengineering

institute: University of California, San Diego

data_processing:
Library strategy: SNARE-seq2
R1/R2 reads and R1/R2/R3 reads.  For R1/R2/R3 reads: R1 = biological, R2 = technical, R3 = biological. R2 contains cellular barcodes sequences.
Deindexer was used to demultiplex reads according to sample barcodes from first round of barcoding for both ATAC and RNA libraries
snaptools 1.4.8 and Minimap2 2.11-r797 to map ATAC libraries
STAR-2.5.1b to map RNA libraries
dropest 0.8.6 to generate RNA count matrices and dropestr to filter cells
ArchR 0.9.4 to generate peak calls and cell by peak matrices
Genome_build: hg38/mm10
Supplementary_files_format_and_content: gz compressed tar archive of features-barcodes matrix

source_name: GM12878 cells

growth_protocol: GM12878 cell line was grown in RPMI-1640 culture medium supplemented with 15% FBS and 2 mM L-glutamine at 37 ºC in a 5% CO2 humidified incubator. A549 cell line was grown in F-12K medium supplemented with 10% FBS at 37 ºC in a 5% CO2 humidified incubator.  NIH/3T3 was grown in Dulbecco’s Modified Eagle’s Medium supplemented with 10% FBS at 37 ºC in a 5% CO2 humidified incubator.

extract_protocol: 1-3 M cells were spun down at 300 g for 5 min at 4C and then washed twice with chilled 1x PBS. Cells were resuspended in 1.2 mL of 1x PBS with RNase Inhibitors (0.04 U/uL SUPERase In RNase Inhibitor, 0.04 U/uL Enzymatics RNase Inhibitors) and filtered through 30 uM CELLTRICS strainers. GM12878 nuclei were extracted from cells with ATAC lysis buffer with 0.1% NP-40 resuspended in 1x PBS with RNase Inhibitors then fixed with 1% formaldehyde. 3T3/A549/GM12878 cells without nuclei extraction were fixed by adding 3 mL of 1.33% formaldehyde and mixed by pipetting followed by incubation on ice for 10 min. GM12878 cells were pelleted at 500 g for 5 min at 4C then resuspended in a resuspension buffer (10 mM Tris-HCl, 10 mM sodium chloride, 3 mM magnesium chloride, 0.04 U/uL SUPERase In RNase Inhibitor, 0.04 U/uL Enzymatics RNase Inhibitors, 0.1% wt/vol BSA) and permeabilized with lysis buffer (10 mM Tris-HCl, 10 mM sodium chloride, 3 mM magnesium chloride, 0.04 U/uL SUPERase In RNase Inhibitor, 0.04 U/uL Enzymatics RNase Inhibitors, 0.1% wt/vol BSA, 0.1% v/v NP-40) for 3 min on ice. 3T3/A549 cells were frozen after fixation in 1x PBS with 10% (v/v) DMSO and 0.1% (wt/vol) BSA for three weeks then washed and permeabilized as described for fresh GM12878 cells. Post permeabilization (or fixation in the case of nuclei), sample were processed using SNARE-seq2 starting from tagmentation step.

treatment_protocol: 3T3 cells amd A549 cells were fixed with 1% formaldehyde and cryopreserved in 1x PBS with 10% (vol/vol) DMSO and 0.1% (wt/vol) BSA for three weeks. GM12878 cells were freshly fixed with 1% formaldeyhyde and ran in two separate experiments. GM12878 nuclei were lysed in cell lysis buffer with RNase Inhibitors (10 mM Tris pH 7.4, 10 mM sodium chloride, 3 mM magnesium chloride, 0.1% v/v NP-40, Superase RNase Inhibitors, Enzymatics RNase Inhibitors) then fixed with 1% formaldehyde. Fixed samples were processed with SNARE-seq2 protocol.

value: GM12878 cells

value: fresh cells were lysed with cell lysis buffer and fixed


title: GM12878 cells exp3 1 processed with SNARE-seq2 protocol (RNAseq)

value: fresh cells were fixed


title: GM12878 cells exp1 processed with SNARE-seq2 protocol (RNAseq)


title: GM12878 cells exp3 2 processed with SNARE-seq2 protocol (RNAseq)


title: GM12878 cells exp3 2 processed with SNARE-seq2 protocol (ATACseq)


title: GM12878 cells exp3 1 processed with SNARE-seq2 protocol (ATACseq)


title: GM12878 nuclei exp2 processed with SNARE-seq2 protocol (ATACseq)


title: SetD_NM_03aph


title: GM12878 cells exp1 processed with SNARE-seq2 protocol (ATACseq)


title: SetE_FX_nt


title: P_38_3: plaPRT_Subject-38_Biopsy-3

status: Public on Sep 08 2020

city: North Chicago

first: Ameya

middle: S

last: Kulkarni

state: Illinois

address: 1 N Waukegan Road

department: Genomics Research Center

institute: AbbVie

data_processing:
Total RNA was sequenced on an Illumina HiSeq 4000 system, using a standard paired-end 150 bp dual indexing protocol. The two sets of samples (University of Kentucky and University of Alabama), each containing samples from all timepoints of both placebo and metformin arm as well as young, were sequenced in different batches that were corrected for in the downstream analyses (see batch).
Raw fastq sequence reads were passed through quality control using FastQC (0.11.4) and the QC results were compiled for all samples using MultiQC (1.7).
Raw fastq files were trimmed for adapter sequences, filtered for low quality reads and short reads, using the default parameters in fastp (0.19.4)
After checking for QC, RNA-Sequencing by Expectation Maximization- RSEM (1.3.0) in conjunction with the STAR aligner (2.6.1b) was used to align the raw reads to the hg38 primary assembly build of the reference human genome, with transcript annotations (gencode.v29.annotation.gtf) downloaded from GENCODE
All statistical analysis for the gene expression data were carried out using the R statistical software (R-3.6.0)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts for each sample (generated using RSEM)

source_name: Vastus lateralis muscle

extract_protocol:
Approximately 35 mg of muscle was subjected to bead homogenization in Qiazol and RNA purified using miRNeasy Mini Kits and stored at -80 C.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Vastus lateralis muscle

tag: study arm

value: plaPRT

tag: biopsy

tag: batch


title: P_37_3: plaPRT_Subject-37_Biopsy-3


title: P_37_1: plaPRT_Subject-37_Biopsy-1


title: P_36_1: plaPRT_Subject-36_Biopsy-1


title: P_31_3: plaPRT_Subject-31_Biopsy-3


title: P_31_1: plaPRT_Subject-31_Biopsy-1


title: P_27_3: plaPRT_Subject-27_Biopsy-3


title: P_26_3: plaPRT_Subject-26_Biopsy-3


title: P_17_3: plaPRT_Subject-17_Biopsy-3


title: P_17_1: plaPRT_Subject-17_Biopsy-1


title: P_11_1: plaPRT_Subject-11_Biopsy-1


title: P_464_3: plaPRT_Subject-464_Biopsy-3


title: P_26_1: plaPRT_Subject-26_Biopsy-1


title: P_18_3: plaPRT_Subject-18_Biopsy-3


title: P_11_3: plaPRT_Subject-11_Biopsy-3


title: P_412_3: plaPRT_Subject-412_Biopsy-3


title: P_413_3: plaPRT_Subject-413_Biopsy-3


title: P_450_1: plaPRT_Subject-450_Biopsy-1


title: P_412_1: plaPRT_Subject-412_Biopsy-1


title: P_464_1: plaPRT_Subject-464_Biopsy-1


title: P_413_1: plaPRT_Subject-413_Biopsy-1


title: P_410_3: plaPRT_Subject-410_Biopsy-3


title: P_38_1: plaPRT_Subject-38_Biopsy-1


title: P_410_1: plaPRT_Subject-410_Biopsy-1


title: P_394_3: plaPRT_Subject-394_Biopsy-3


title: SetE_FX_03aph


title: P_394_1: plaPRT_Subject-394_Biopsy-1


title: P_364_1: plaPRT_Subject-364_Biopsy-1


title: P_36_3: plaPRT_Subject-36_Biopsy-3


title: P_329_1: plaPRT_Subject-329_Biopsy-1


title: P_270_1: plaPRT_Subject-270_Biopsy-1


title: P_27_1: plaPRT_Subject-27_Biopsy-1


title: P_198_1: plaPRT_Subject-198_Biopsy-1


title: P_18_1: plaPRT_Subject-18_Biopsy-1


title: P_081_1: plaPRT_Subject-081_Biopsy-1


title: P_206_1: plaPRT_Subject-206_Biopsy-1


title: P_086_3: plaPRT_Subject-086_Biopsy-3


title: P_080_3: plaPRT_Subject-080_Biopsy-3


title: P_048_3: plaPRT_Subject-048_Biopsy-3


title: P_080_1: plaPRT_Subject-080_Biopsy-1


title: P_169_1: plaPRT_Subject-169_Biopsy-1


title: P_048_1: plaPRT_Subject-048_Biopsy-1


title: P_012_1: plaPRT_Subject-012_Biopsy-1


title: P_081_3: plaPRT_Subject-081_Biopsy-3


title: P_086_1: plaPRT_Subject-086_Biopsy-1


title: P_008_1: plaPRT_Subject-008_Biopsy-1


title: GM12878_24hr_R2_HiC

status: Public on Sep 04 2020

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee,Knoxville

data_processing:
Sequenced reads were mapped to the hg19 genome using bowtie2
Filtering was carried out using the dekkerlab-cMapping pipeline available on github
Iterative correction was performed using method described by Imakaev et al.
All processed Hi-C contact maps were scaled to a sum of 1 million
Genome_build: hg19
Supplementary_files_format_and_content: each .tar file contains the iteratively corrected and raw matrix.gz files for 40 kb, 250 kb, and 2.5 Mb in their respective directories

growth_protocol: Fibroblast lines were grown to confluency prior to X-ray exposure. For the GM12878 suspension cell line, cells were passaged at a density around 500,000 cells per 1 mL of medium. For irradiation experiments, GM12878 cells were grown to a density of 1 million cells per 1 mL of medium prior to X-ray exposure.

extract_protocol:
Briefly, 5-20 million cells were fixed with 1% formaldehyde, suspended in cell lysis buffer for permeabilization, and homogenized by douncing. Crosslinked chromatin was digested overnight with HindIII. Sticky ends were filled in with biotin-dCTP, and the blunt ends of interacting fragments were ligated together. DNA was purified by two phenol-chloroform extractions and ethanol precipitation. Biotin-dCTP at unligated ends was removed, and the DNA was sheared to a target size of 200-400 bp by a Covaris sonicator
Biotinylated DNA was pulled down using streptavidin coated magnetic beads and prepared for multiplex sequencing on an Illumina platform using the NEBNext Ultra II kit (NEB). All end preparation, adaptor ligation, and PCR amplification steps were carried out on bead bound DNA libraries.

treatment_protocol: Treated cells were X-rayed using 5 Gy X-rays and fixed for Hi-C after 30 mins, 24 hours, or split after 24 hours and allowed to recover for 5 days. The treated cells and their control counterparts were then fixed for Hi-C. ATM inhibitor treated cells were subjected to 10um KU-55933 for 1 hour before experiment began. ATMiC was subjected to KU-55933, but not IR.

value: Lymphoblastoid

tag: condition

tag: media


title: GM12878_24hr_R1_HiC


title: P_015_1: plaPRT_Subject-015_Biopsy-1


title: GM12878_Control_R2_HiC

value: Control


title: GM12878_Control_R1_HiC


title: P_284_3: plaPRT_Subject-284_Biopsy-3


title: GM12878_30min_R2_HiC


title: GM12878_30min_R1_HiC


title: GM02052_24hr_R1_HiC

value: Skin fibroblast


title: P_284_1: plaPRT_Subject-284_Biopsy-1


title: GM02052_Control_R1_HiC


title: RNA-seq_hMGL SORL1-A528T Rep7

status: Public on Sep 01 2020

first: Timothy

last: Huang

address: 10901 N. Torrey Pines Rd

institute: SBP Medical Discovery Institute

data_processing:
Adapter remnants from sequencing reads were removed using cutadapt v1.18 (Martin, 2011). RNA-Seq sequencing reads were aligned using STAR aligner version 2.7 (Dobin et al., 2013). Human genome version 38 and Ensembl gene annotation version 84 were used in the alignment and quantification. Quantification was performed based on RSEM v1.3.1 (Li and Dewey, 2011). Estimated read counts from RSEM were compared using the R Bioconductor package DESeq2 following generalized linear model based on negative binomial distribution. Genes with Benjamini-Hochberg–corrected p value< 0.1 were selected as significantly differentially expressed genes.
Genome_build: Human genome version 38 and Ensembl gene annotation version 84
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

source_name: Human ES-derived microglia-like cell lines (hMGLs)

growth_protocol: hESC H9 cells (WA09) used in this study was purchased from the WiCell Research Institute. Undifferentiated human ESCs were maintained using the Feeder Independent Culture Platform- TeSR-E8/Matrigel™. Human ESCs-derived hMGLs were generated using recently published protocols (McQuade et al., 2018). Differentiation of parental H9 to CD43+ primitive hematopoietic progenitor cells (HPCs) was performed using Stem Cell Technologies STEMdiffTM Hematopoietic Kit (Catalog # 05310). H9 cells were seeded into 35mm wells with mTeSR-E8 medium at a density of 60 colonies of 100 cells. On day 0, cells were switched from STEMdiff Hematopoietic Kit (Stem Cell Technologies) to Medium A. On day 3, cell colonies were changed to Medium B for 7 additional days, during which, HPCs separated from the colonies. At day 11, HPCs were collected and plated at a density of 10,000 cells per cm2 onto 1 mg/mL Matrigel-coated plates. Microglial differentiation was induced over 28 days by feeding the HPCs every other day with differentiation medium (DMEM/F12, 2X insulin-transferrin-selenite, 2X B27, 0.5X N2, 1X glutamax, 1X non-essential amino acids, 400 mM monothioglycerol, and 5 mg/mL human insulin freshly supplemented with 100 ng/mL IL-34, 50 ng/mL TGF1, and 25 ng/mL M-CSF (Peprotech)). During the final 3 days of differentiation, 100 ng/mL CD200 (Novoprotein) and 100 ng/mL CX3CL1 (Peprotech), were added to mature microglia to mimic a brain-like environment.

extract_protocol:
After washing with cold PBS, hMGLs were lysed using TRIzol® Reagent (Thermo fisher, Cat # 15596026) and stored at -80C for RNA extraction. Total RNA was extracted using the RNeasy Plus Micro Kit (50) (QIAGEN #74034), following manufacturer’s recommendations with slight adjustment. Briefly, 200 ul of chloroform was added to the TRIzol extraction solution/cells, mixed, and centrifuged. RNa was then extracted from the aqueous phase according to the manufacturer’s recommendations. RNA was quantified using a NanoDrop spectrophotometer and RNA integrity numbers (RINs) were assessed using an Agilent TapeStation 4200 system; all samples used for subsequent analysis showed a minimum RIN of 9 or 10.
For each replicate, RNA-seq libraries were prepared from 500 ng of purified total RNA using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA) following manufacturer’s recommendations, and sequenced on an Illumina Hisdeq platform as paired end 150-bp reads (Genewiz, LLC, South Plainfield, NJ). An average sequencing depth of 45.13 M (±3.6 M) was obtained in from the hMGL samples, with minimum and maximum values of 39.2 and 64.6 M.

treatment_protocol: Single guide RNAs (sgRNAs) and primers for PCR amplification and detection of off-target sites were designed using the Zhang laboratory CRISPR design tool (http://crispr.mit.edu) or Benchling [Biology Software] (2019) (https://benchling.com). sgRNA sequences targeting genes or SNP loci (Table S1) were cloned into PX458 (Addgene plasmid ID: 48138) as previously described (Ran et al., 2013). The 100-nt single-stranded oligodeoxynucleotide (ssODN) repair templates (PAGE-purified, IDT) were designed with homologous genomic flanking sequence centered around the predicted CRISPR/Cas9 cleavage site. Human ESC (hESC) H9 cells were transfected with PX458 containing sgRNAs and ssODNs. FACS isolation of hESC clones, genomic DNA extraction, clone screening and off-target analysis were performed as described previously (Ran et al., 2013). All CRISPR/Cas9 modifications converted H9 genome sequences to homozygous AD-associated variants for CD33 SNP, INPP5D SNP, TREM2 KO, TREM2R47H, SORL1R744X and SORL1A528T. H9 was endogenously heterozygous for the INPP5D G/A polymorphism, and was converted homozygously to the “A” allele. A sgRNA was designed targeting a site proximal to the CX3CR1 stop codon and generating a double stranded break (DSB). This DSB is repaired through homologous recombination of the donor plasmid, resulting in an in-frame insertion of 2A-EGFP downstream of the CX3CR1 terminal exon. Using control, isogenic TREM2R47H and SORL1R744X lines, we created three GFP-expressing reporter lines specifically suited for live two-photon microscopy.

tag: genotype


title: RNA-seq_hMGL SORL1-KO Rep7

tag: cell type

value: Human ES-derived microglia-like cell lines (hMGLs)


title: RNA-seq_hMGL TREM2-R47H Rep7


title: RNA-seq_hMGL TREM2-KO Rep8


title: RNA-seq_hMGL TREM2-KO Rep7


title: RNA-seq_hMGL WT Rep7

value: WT


title: RNA-seq_hMGL SORL1-KO Rep6


title: RNA-seq_hMGL TREM2-R47H Rep6


title: RNA-seq_hMGL SORL1-A528T Rep6


title: RNA-seq_hMGL TREM2-KO Rep6


title: RNA-seq_hMGL SORL1-A528T Rep5


title: RNA-seq_hMGL SORL1-KO Rep5


title: RNA-seq_hMGL WT Rep6


title: RNA-seq_hMGL TREM2-R47H Rep5


title: RNA-seq_hMGL TREM2-KO Rep5


title: RNA-seq_hMGL INPP5D Rep2

value: INPP5D SNP


title: RNA-seq_hMGL CD33 Rep2

value: CD33 SNP


title: RNA-seq_hMGL TREM2-R47H Rep4


title: RNA-seq_hMGL SORL1-A528T Rep4


title: RNA-seq_hMGL WT Rep5


title: RNA-seq_hMGL SORL1-KO Rep4


title: RNA-seq_hMGL INPP5D Rep1


title: RNA-seq_hMGL CD33 Rep1


title: RNA-seq_hMGL TREM2-KO Rep4


title: P_012_3: plaPRT_Subject-012_Biopsy-3


title: RNA-seq_hMGL TREM2-KO Rep3


title: RNA-seq_hMGL WT Rep4


title: RNA-seq_hMGL SORL1-A528T Rep3


title: RNA-seq_hMGL TREM2-R47H Rep3


title: RNA-seq_hMGL WT Rep3


title: RNA-seq_hMGL SORL1-KO Rep3


title: RNA-seq_hMGL SORL1-A528T Rep2


title: RNA-seq_hMGL SORL1-KO Rep2


title: RNA-seq_hMGL WT Rep2


title: RNA-seq_hMGL SORL1-A528T Rep1


title: RNA-seq_hMGL TREM2-KO Rep2


title: RNA-seq_hMGL TREM2-R47H Rep2


title: RNA-seq_hMGL SORL1-KO Rep1


title: RNA-seq_hMGL TREM2-KO Rep1


title: RNA-seq_hMGL TREM2-R47H Rep1


title: hMGL SORL1-A528T Input Rep2

data_processing:
Adapter remnants of sequencing reads were removed using cutadapt v1.18 (Martin, 2011). ChIP-Seq sequencing reads were aligned using STAR aligner version 2.7 to Human genome version 38 (Dobin et al., 2013). Homer v4.10 (Heinz et al., 2010) was used to call peaks from ChIP-Seq samples, annotate peaks to human genes, and quantify reads count to peaks. The raw reads count for different peaks were compared using DESeq2 (Love et al., 2014) based on generalized linear model adjusting for batch effect. Peaks with p value< 0.05 and fold change >=1.5 or <=2⁄3 were selected as significantly differentially marked peaks. Genes associated with any differentially marked peaks at exon, intron, promoter, transcription termination site (TTS), and closest intergenic region were investigated for Gene Ontology and pathway functional enrichment tests.
Genome_build: Human genome version 38 and Ensembl gene annotation version 84
Supplementary_files_format_and_content: ChIP-Seq peaks called by Homer
Supplementary_files_format_and_content: BigWig file and peak files

extract_protocol:
hMGLs were detached by accutase digestion and rinsed twice with PBS. Cells were pelleted in 1.5 ml Eppendorf tubes and fixed using 1 ml 1% formaldehyde (Sigma, F8775, St Louis, MO) diluted in PBS at room temperature for 10 min. Formaldehyde was quenched by adding a Glycine solution to a final concentration of 125 mM and incubated for 5 min at room temperature. After washing twice with 1 ml PBS, 1 ml cell lysis buffer was added to the cell pellet, incubated for 10 min on ice, and further lysed in lysis buffer (iL2). Chromatin was resuspended in 130 ml Shearing buffer and sheared using a Covaris S220 sonicator to 200-500 bp (Duty cycle 2% for 10 min) in an M220 microTUBE (Covaris, 520077). Equal aliquots of sonicated chromatin were used per immunoprecipitation reaction comprising 2 ml H3K27ac antibody (Abcam, Ab4729), H3K4me3 antibody (Millipore, 07-472), or 2 ml Rabbit IgG control antibody (Diagenode) and 1 ml sheared chromatin as input. The total volume of each ChIP reaction was 300 ml, and included 6 ml 5% BSA, 1.5 ml 200 x protease inhibitor cocktail, 56 ml 5 x buffer iC1, 20 ml magnetic beads, 2 ml antibody and sonicated chromatin. ChIP reactions were incubated overnight at 4 °C under constant rotation. Magnetic beads (conjugated with antibody-histone-DNA) were washed with 350 ml buffer iW1, iW2, iW3, and iW4. Precipitated chromatin was eluted in 100 ml Elution buffer iE1 for 30 min at room temperature under constant agitation, and transferred into a 200 ml tube. Chromatin crosslinks were uncoupled by adding 4 ml of Elution buffer iE2 and incubating for 4 h at 65°C. DNA was isolated using IPure beads v2 and eluted in 25 ml Elution buffer. 10 ml precipitated DNA was further processed for template preparation, library synthesis, and library amplification. Amplified products were purified, and size selected using AMPure XP beads (Beckman Coulter, A63880). All libraries were quantified using an Agilent 2100 Bioanalyzer
Samples were pooled/sequenced using a NextSeq 500/550 High Output v2 kit using paired-end reads on a NextSeq 500 platform (Illumina).

value: Rabbit IgG control antibody


title: hMGL SORL1-KO Input Rep1


title: hMGL SORL1-A528T Input Rep1


title: hMGL TREM2-R47H Input Rep2


title: hMGL SORL1-KO Input Rep2


title: hMGL INPP5D SNP Input Rep1


title: RNA-seq_hMGL WT Rep1


title: hMGL TREM2-R47H Input Rep1


title: hMGL TREM2-KO Input Rep2


title: hMGL TREM2-KO Input Rep1


title: hMGL CD33 SNP Input Rep2


title: hMGL INPP5D SNP Input Rep2


title: hMGL WT Input Rep2


title: hMGL CD33 SNP Input Rep1


title: hMGL SORL1-KO H3K27ac Rep1


title: hMGL SORL1-A528T H3K27ac Rep1


title: hMGL SORL1-A528T H3K27ac Rep2


title: hMGL TREM2-R47H H3K27ac Rep2


title: hMGL TREM2-R47H H3K27ac Rep1


title: hMGL INPP5D SNP H3K27ac Rep2


title: hMGL INPP5D SNP H3K27ac Rep1


title: hMGL TREM2-KO H3K27ac Rep1


title: hMGL WT H3K27ac Rep2


title: hMGL CD33 SNP H3K27ac Rep1


title: hMGL CD33 SNP H3K27ac Rep2


title: hMGL TREM2-KO H3K27ac Rep2


title: hMGL SORL1-A528T H3K4me3 Rep2


title: hMGL WT H3K27ac Rep1


title: hMGL SORL1-KO H3K4me3 Rep2


title: hMGL SORL1-A528T H3K4me3 Rep1


title: hMGL SORL1-KO H3K4me3 Rep1


title: hMGL TREM2-R47H H3K4me3 Rep1


title: hMGL WT Input Rep1


title: hMGL TREM2-R47H H3K4me3 Rep2


title: hMGL SORL1-KO H3K27ac Rep2


title: hMGL TREM2-KO H3K4me3 Rep2


title: hMGL INPP5D SNP H3K4me3 Rep1


title: hMGL INPP5D SNP H3K4me3 Rep2


title: hMGL WT H3K4me3 Rep1


title: hMGL CD33 SNP H3K4me3 Rep1


title: hMGL CD33 SNP H3K4me3 Rep2


title: hMGL TREM2-KO Rep2

data_processing:
Adapter remnants of sequencing reads were removed using cutadapt v1.18 (Martin, 2011). ATAC-Seq sequencing reads were aligned using STAR aligner version 2.7 to Human genome version 38 (Dobin et al., 2013). Homer v4.10 (Heinz et al., 2010) was used to call peaks from ATAC-Seq samples, annotate peaks to human genes, and quantify reads count to peaks. The raw reads count for different peaks were compared using DESeq2 (Love et al., 2014) based on generalized linear model adjusting for batch effect. Peaks with p value< 0.05 and fold change >=1.5 or <=2⁄3 were selected as significantly differentially marked peaks. Genes associated with any differentially marked peaks at exon, intron, promoter, transcription termination site (TTS), and closest intergenic region were investigated for Gene Ontology and pathway functional enrichment tests.
Genome_build: Human genome version 38 and Ensembl gene annotation version 84
Supplementary_files_format_and_content: ATAC-Seq peaks called using Homer
Supplementary_files_format_and_content: BigWig files and peak files

extract_protocol:
ATAC-seq analysis was performed using the Omni-ATAC-seq protocol (Corces et al., 2017). Briefly, 80,000 viable hMGLs per line were sorted using BD FACSAriaIIu 16-color high-speed cell sorter. Cells were lysed in 50 ml ATAC-Resuspension Buffer containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin and incubated on ice for 3 min. After washing with ATAC-RSB buffer (without NP40), nuclei were pelleted by centrifugation and incubated in 50 ml transposition mixture (25 ml 2 x TD buffer (Illumina, Ref 15027866), 2.5 ml transposase (Illumina, Ref 15027865), 16.5 ml PBS, 0.5 ml 1% digitonin, 0.5 ml 10% Tween-20, 5 ml H2O) at 37 °C for 30 min. Transposed DNA was purified using a Zymo DNA clean and concentrator-5 kit (Zymo research, Cat. No. D4014). Purified DNA was subjected to PCR amplification using the NEBNext® High-Fidelity 2 x PCR Master Mix (NEB, Cat. No. M0541s) system for first 5, and subsequent 3 cycles. Primer adapters were synthesized by IDT (Integrated DNA technology). Libraries were purified using a Zymo DNA clean and concentrator-5 kit, size-selected using AMPure XP beads, quantified using an Agilent 2100 Bioanalyzer
Samples were pooled/sequenced using a NextSeq 500/550 High Output v2 kit using paired-end reads on a NextSeq 500 platform (Illumina).


title: hMGL TREM2-KO Rep1


title: hMGL WT Rep2


title: hMGL TREM2-KO Rep3


title: hMGL WT Rep1


title: hMGL TREM2-R47H Rep1


title: hMGL TREM2-R47H Rep3


title: hMGL INPP5D Rep1


title: hMGL INPP5D Rep2


title: hMGL INPP5D Rep3


title: hMGL CD33 Rep3


title: hMGL TREM2-KO H3K4me3 Rep1


title: hMGL SORL1-KO Rep1


title: hMGL TREM2-R47H Rep2


title: hMGL WT Rep3


title: hMGL SORL1-A528T Rep3


title: hMGL SORL1-A528T Rep2


title: hMGL SORL1-A528T Rep1


title: hMGL WT H3K4me3 Rep2


title: hMGL CD33 Rep2


title: lung_M2

status: Public on Aug 31 2020

city: Chicago

first: Joyce

middle: huanhuan

last: Chen

state: IL

address: 5801 S Ellis Ave, Chicago

department: Pritzker School of Molecular Engineering

institute: Uchicago

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference genome (GRCh38 v3.0.0) plus virus sequence and to extract gene expression UMI counts matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: RUES2-derived lung cells and M2 macrophages co-culture

growth_protocol: RUES2 cells were differentiated to endoderm, anterior foregut endoderm, lung progenitor cells and functional lung cells using growth factor cocktails inclduing Activin A, CHIR, DSW, IWP2, FGF10, KFG, DAPT  etc.RUES2 cells were differentiated to  functional macrophages using growth factor cocktails inclduing BMP, CHIR, FGF2,VEGF,SB431542,IL3,M-CSF  etc

extract_protocol:
Single-cell suspensions were generated by dissociating the cultured RUES2 cells with 0.05% Trypsin/0.02% EDTA for 10-15 min, followed with passing through 40µM strainer.
Single-cell capture, reverse transcription, cell lysis, and library preparation was performed using the Single Cell 3' version 2 kit and chip according to the manufacturer’s protocol (10x Genomics)
scRNA-seq

treatment_protocol: For macrophage polarization, monocytes from differentiating day13-15 were treated with 10ng/ml IFNγ+100ng/ml LPS to genarate M1 macrophages, 20ng/ml IL4 to generate M2 macrophages,respectively. To assay pseudotyped virus infection on co-culture system, Pseudotyped virus was added at MOI=0.01 plus polybrene at a final concentration of 8 μg/mL for 30hrs.


title: lung_control

source_name: RUES2-derived lung cells

value: RUES2-derived lung cells


title: hMGL SORL1-KO Rep3


title: hMGL CD33 Rep1


title: lung_M1

source_name: RUES2-derived lung cells and M1 macrophages co-culture


title: CAD_NA766PT_RNA_2151A_C7

status: Public on Aug 28 2020

type: RNA

city: New York

first: Zhengming

address: 402 67th street

institute: Weill Cornell Medicine

description: Lung cancer patient who underwent surgery for early stage lung cancer and for whom no neoadjuvant or adjuvant therapy was used.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133_Plus_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Squamous Cell Carcinoma of Lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: A histological H&E slide was made from frozen material adjacent to the portion from each tumor used to prepare 2 ug of total RNA. The slides were sent to the pathology core at the University of Colorado for review of histology and tumor content, the RNA was robotically prepared by the Duke core lab. Following RNA isolation with Trizol (Invitrogen) and miRNeasy column (Qiagen), RNA yield and purity is assessed by the Nanodrop, RNA integrity is determined by an Agilent 2100 Bioanalyzer and the concentration is calculated by OD260 measurement. Chip quality was assessed with the Affymetrix Microarray Suite and Mining Tools.

tag: diagnosis

value: Squamous Cell Carcinoma of Lung

value: lung

tag: age

tag: Sex

value: Female

tag: Stage


title: CAD_NA740PT_RNA_2144A_F5

value: Male


title: CAD_NA765PT_RNA_2151A_C4


title: CAD_NA734PT_RNA_2144A_A8


title: CAD_NA735PT_RNA_2151A_E4


title: CAD_NA738PT_RNA_2151A_D7


title: CAD_NA737PT_RNA_2144A_B12


title: CAD_NA736PT_RNA_2144A_A12


title: CAD_NA731PT_RNA_2144A_F2


title: CAD_NA732PT_RNA_2151A_D4


title: CAD_NA712PT_RNA_2151A_E1


title: CAD_NA726PT_RNA_2144A_H11


title: CAD_NA717PT_RNA_2144A_G11


title: CAD_NA714PT_RNA_2144A_G7


title: CAD_NA721PT_RNA_2151A_D5


title: CAD_NA716PT_RNA_2151A_H6


title: CAD_NA715PT_RNA_2144A_E5


title: CAD_NA733PT_RNA_2144A_H7


title: CAD_NA718PT_RNA_2151A_B2


title: CAD_NA722PT_RNA_2151A_E5


title: hMGL SORL1-KO Rep2


title: CAD_NA720PT_RNA_2151A_A7


title: CAD_NA723PT_RNA_2151A_F5


title: CAD_NA728PT_RNA_2151A_G5


title: CAD_NA708PT_RNA_2151A_C5


title: CAD_NA710PT_RNA_2151A_D1


title: CAD_NA711PT_RNA_2144A_F7


title: CAD_NA709PT_RNA_2151A_C1


title: CAD_NA705PT_RNA_2151A_B5


title: CAD_NA703PT_RNA_2144A_D7


title: CAD_NA687PT_RNA_2144A_D4


title: CAD_NA690PT_RNA_2144A_F12


title: CAD_NA692PT_RNA_2151A_G6


title: CAD_NA706PT_RNA_2144A_E7


title: CAD_NA696PT_RNA_2151A_G3


title: CAD_NA691PT_RNA_2151A_G1


title: CAD_NA689PT_RNA_2144A_E12


title: CAD_NA684PT_RNA_2144A_D12


title: CAD_NA683PT_RNA_2144A_C12


title: CAD_NA695PT_RNA_2151A_A2


title: CAD_NA701PT_RNA_2151A_A1


title: CAD_NA681PT_RNA_2144A_G5


title: CAD_NA678PT_RNA_2144A_F9


title: CAD_NA685PT_RNA_2144A_H2


title: CAD_NA680PT_RNA_2144A_G9


title: CAD_NA713PT_RNA_2151A_F1


title: CAD_NA693PT_RNA_2151A_H1


title: CAD_NA698PT_RNA_2151A_B7


title: CAD_NA699PT_RNA_2151A_B1


title: CAD_NA686PT_RNA_2144A_B8


title: CAD_NA694PT_RNA_2151A_F3


title: CAD_NA677PT_RNA_2144A_C4


title: CAD_NA682PT_RNA_2144A_G2


title: CAD_NA688PT_RNA_2144A_A3


title: CAD_NA679PT_RNA_2144A_C7


title: CAD_NA676PT_RNA_2144A_B4


title: CAD_NA675PT_RNA_2144A_E2


title: CAD_NA672PT_RNA_2144A_E9


title: CAD_NA548PT_RNA_2152A_D3


title: CAD_NA557PT_RNA_2124A_H1


title: CAD_NA673PT_RNA_2144A_D5_RR1


title: CAD_NA556PT_RNA_2124A_F6


title: CAD_NA674PT_RNA_2144A_D2


title: CAD_NA539PT_RNA_2119A_D9


title: CAD_NA553PT_RNA_2152A_D1


title: CAD_NA537PT_RNA_2119A_C9


title: CAD_NA670PT_RNA_2144A_B7


title: CAD_NA535PT_RNA_2119A_H5


title: CAD_NA551PT_RNA_2124A_F11


title: CAD_NA546PT_RNA_2124A_C1


title: CAD_NA547PT_RNA_2124A_E5


title: CAD_NA538PT_RNA_2119A_A8


title: CAD_NA544PT_RNA_2119A_E8


title: CAD_NA552PT_RNA_2124A_E1


title: CAD_NA555PT_RNA_2124A_E6


title: CAD_NA543PT_RNA_2119A_E9


title: CAD_NA541PT_RNA_2119A_C8


title: CAD_NA550PT_RNA_2124A_F8


title: CAD_NA542PT_RNA_2119A_D8


title: CAD_NA549PT_RNA_2124A_D1


title: CAD_NA669PT_RNA_2144A_A4


title: CAD_NA554PT_RNA_2124A_G1


title: CAD_NA671PT_RNA_2144A_C5


title: CAD_NA545PT_RNA_2119A_E11


title: CAD_NA536PT_RNA_2119A_A6


title: CAD_NA540PT_RNA_2119A_B8


title: CAD_NA525PT_RNA_2119A_F12


title: CAD_NA532PT_RNA_2152A_E2


title: CAD_NA531PT_RNA_2119A_E10


title: CAD_NA514PT_RNA_2119A_C11


title: CAD_NA515PT_RNA_2119A_H8


title: CAD_NA524PT_RNA_2119A_B9


title: CAD_NA530PT_RNA_2119A_F5


title: CAD_NA520PT_RNA_2119A_G10


title: CAD_NA529PT_RNA_2119A_H7


title: CAD_NA516PT_RNA_2119A_A9


title: CAD_NA513PT_RNA_2119A_B11


title: CAD_NA730PT_RNA_2151A_C2


title: CAD_NA522PT_RNA_2119A_E12


title: CAD_NA518PT_RNA_2119A_B10


title: CAD_NA507PT_RNA_2119A_C12


title: CAD_NA512PT_RNA_2119A_D12


title: CAD_NA523PT_RNA_2119A_G7


title: CAD_NA528PT_RNA_2119A_C10


title: CAD_NA534PT_RNA_2119A_G5


title: CAD_NA521PT_RNA_2119A_F7


title: CAD_NA517PT_RNA_2119A_E7


title: CAD_NA510PT_RNA_2119A_D7


title: CAD_NA533PT_RNA_2119A_D11


title: CAD_NA527PT_RNA_2119A_D10


title: CAD_NA519PT_RNA_2119A_D5


title: CAD_NA509PT_RNA_2119A_A10


title: CAD_NA506PT_RNA_2119A_C7


title: CAD_NA526PT_RNA_2119A_E5


title: CAD_NA505PT_RNA_2119A_C5


title: CAD_NA493PT_RNA_2119A_E6


title: CAD_NA494PT_RNA_2119A_A5


title: CAD_NA499PT_RNA_2119A_A12


title: CAD_NA503PT_RNA_2119A_B7


title: CAD_NA504PT_RNA_2119A_B5


title: CAD_NA498PT_RNA_2119A_H6


title: CAD_NA501PT_RNA_2119A_B12


title: CAD_NA497PT_RNA_2119A_H11


title: CAD_NA495PT_RNA_2119A_F6


title: CAD_NA485PT_RNA_2119A_F10


title: CAD_NA502PT_RNA_2119A_A7


title: CAD_NA500PT_RNA_2119A_H9


title: CAD_NA480PT_RNA_2119A_F4


title: CAD_NA487PT_RNA_2119A_G11


title: CAD_NA484PT_RNA_2119A_C6


title: CAD_NA496PT_RNA_2119A_G6


title: CAD_NA489PT_RNA_2119A_G8


title: CAD_NA511PT_RNA_2119A_A11


title: CAD_NA481PT_RNA_2119A_B6


title: CAD_NA508PT_RNA_2119A_H10


title: CAD_NA479PT_RNA_2116A_F12


title: CAD_NA482PT_RNA_2119A_G9


title: CAD_NA492PT_RNA_2119A_D6


title: CAD_NA490PT_RNA_2119A_H4


title: CAD_NA483PT_RNA_2119A_F11


title: CAD_NA488PT_RNA_2119A_F8


title: CAD_NA478PT_RNA_2116A_C5


title: CAD_NA469PT_RNA_2116A_A9


title: CAD_NA473PT_RNA_2116A_G10


title: CAD_NA462PT_RNA_2116A_D10


title: CAD_NA471PT_RNA_2116A_C7


title: CAD_NA472PT_RNA_2116A_F10


title: CAD_NA461PT_RNA_2116A_G6


title: CAD_NA457PT_RNA_2116A_B5


title: CAD_NA460PT_RNA_2116A_F11


title: CAD_NA459PT_RNA_2116A_F6


title: CAD_NA470PT_RNA_2116A_B7


title: CAD_NA458PT_RNA_2116A_E6


title: CAD_NA463PT_RNA_2116A_H6


title: CAD_NA466PT_RNA_2116A_H8


title: CAD_NA456PT_RNA_2116A_A5


title: CAD_NA464PT_RNA_2116A_E10


title: CAD_NA486PT_RNA_2119A_G4


title: CAD_NA455PT_RNA_2116A_H4


title: CAD_NA451PT_RNA_2116A_F4


title: CAD_NA450PT_RNA_2116A_E4


title: CAD_NA447PT_RNA_2116A_B4


title: CAD_NA446PT_RNA_2116A_A4


title: CAD_NA468PT_RNA_2116A_D11


title: CAD_NA453PT_RNA_2116A_D6


title: CAD_NA449PT_RNA_2116A_D4


title: CAD_NA454PT_RNA_2116A_C10


title: CAD_NA467PT_RNA_2116A_A7


title: CAD_NA452PT_RNA_2116A_G4


title: CAD_NA448PT_RNA_2116A_C4


title: CAD_NA445PT_RNA_2116A_H3


title: CAD_NA465PT_RNA_2116A_C11


title: CAD_NA443PT_RNA_2116A_C6


title: CAD_NA444PT_RNA_2116A_G3


title: CAD_NA431PT_RNA_2116A_A11


title: CAD_NA434PT_RNA_2116A_C3


title: CAD_NA441PT_RNA_2116A_E3


title: CAD_NA433PT_RNA_2116A_B3


title: CAD_NA442PT_RNA_2116A_F3


title: CAD_NA436PT_RNA_2116A_F8


title: CAD_NA439PT_RNA_2116A_B6


title: CAD_NA438PT_RNA_2116A_G8


title: CAD_NA429PT_RNA_2116A_A3


title: CAD_NA428PT_RNA_2116A_H2_RR1


title: CAD_NA437PT_RNA_2116A_A6


title: CAD_NA432PT_RNA_2116A_B11


title: CAD_NA440PT_RNA_2116A_D3


title: CAD_NA435PT_RNA_2116A_H5


title: CAD_NA426PT_RNA_2116A_E8


title: CAD_NA427PT_RNA_2116A_E11


title: CAD_NA421PT_RNA_2116A_C8


title: CAD_NA420PT_RNA_2116A_F5


title: CAD_NA430PT_RNA_2116A_H10


title: CAD_NA419PT_RNA_2116A_E2_RR1


title: CAD_NA425PT_RNA_2116A_G5


title: CAD_NA417PT_RNA_2116A_B10


title: CAD_NA415PT_RNA_2116A_C2_RR1


title: CAD_NA416PT_RNA_2116A_D2_RR1


title: CAD_NA422PT_RNA_2152A_C1


title: CAD_NA406PT_RNA_2116A_F9


title: CAD_NA412PT_RNA_2116A_A10


title: CAD_NA401PT_RNA_2116A_G1_RR1


title: CAD_NA424PT_RNA_2116A_D8


title: CAD_NA404PT_RNA_2116A_D9


title: CAD_NA402PT_RNA_2116A_A8


title: CAD_NA397PT_RNA_2116A_G11


title: CAD_NA407PT_RNA_2116A_G9


title: CAD_NA399PT_RNA_2116A_H7


title: CAD_NA413PT_RNA_2116A_B8


title: CAD_NA388PT_RNA_2116A_D5


title: CAD_NA403PT_RNA_2116A_H1_RR1


title: CAD_NA400PT_RNA_2116A_C9


title: CAD_NA405PT_RNA_2116A_E9


title: CAD_NA418PT_RNA_2116A_E5


title: CAD_NA408PT_RNA_2116A_B12


title: CAD_NA396PT_RNA_2116A_E1_RR1


title: CAD_NA395PT_RNA_2116A_E12


title: CAD_NA414PT_RNA_2116A_B2_RR1


title: CAD_NA387PT_RNA_2116A_E7


title: CAD_NA410PT_RNA_2116A_A2_RR1


title: CAD_NA391PT_RNA_2116A_F7


title: CAD_NA398PT_RNA_2116A_F1_RR1


title: CAD_NA394PT_RNA_2116A_D1_RR1


title: CAD_NA411PT_RNA_2116A_H9


title: CAD_NA393PT_RNA_2116A_G7


title: CAD_NA389PT_RNA_2116A_D12


title: CAD_NA386PT_RNA_2116A_B1_RR1


title: CAD_NA384PT_RNA_2115A_E4


title: CAD_NA383PT_RNA_2115A_E7


title: CAD_NA385PT_RNA_2115A_G5


title: CAD_NA390PT_RNA_2116A_A12


title: CAD_NA379PT_RNA_2115A_F4


title: CAD_NA380PT_RNA_2115A_H1


title: CAD_NA382PT_RNA_2115A_G4


title: WAU375

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.


title: WAU346


title: WAU341


title: CAD_NA381PT_RNA_2115A_C3


title: WAU372


title: WAU335


title: BWH228


title: WAU360


title: BWH232


title: BWH238


title: WAU330


title: WAU323


title: WAU368


title: BWH220


title: WAU364


title: WAU367


title: BWH217


title: BWH231


title: WAU370


title: WAU349


title: WAU307


title: WAU309


title: WAU347


title: UCD026


title: WAU302


title: WAU340


title: WAU350


title: PMH517


title: UCD030


title: WAU324


title: UCD031


title: WAU351


title: UCD036


title: PMH543


title: UCD027


title: PMH509


title: PMH542


title: PMH540


title: PMH526


title: PMH507


title: PMH524


title: PMH506


title: PMH539


title: PMH505


title: PMH538


title: CAD_NA392PT_RNA_2116A_C1_RR1


title: PMH514


title: PMH537


title: PMH513


title: PMH503


title: PMH522


title: PMH516


title: PMH536


title: UCD037


title: PMH501


title: UM145


title: PMH510


title: UM136


title: PMH544


title: UM127


title: PMH502


title: PMH519


title: PMH520


title: UM144


title: PMH512


title: UM126


title: UM117


title: UM153


title: UM125


title: UM118


title: UM143


title: UM116


title: UM134


title: UM151


title: UM154


title: UM135


title: UM108


title: UM152


title: UM115


title: UM106


title: UM133


title: UM107


title: UM141


title: UM124


title: UM150


title: UM123


title: UM140


title: UM142


title: PMH545


title: UM121


title: UM104


title: UM130


title: UM131


title: UM113


title: UM105


title: UM112


title: UM139


title: UM122


title: UM103


title: UM120


title: UM129


title: UM148


title: UM102


title: UM155


title: UM146


title: UM137


title: UM101


title: UM110


title: UM119


title: UM147


title: WAU317


title: UM128


title: DUK470


title: DUK439


title: DUK432


title: DUK407


title: DUK455


title: DUK426


title: DUK406


title: WAU316


title: DUK438


title: DUK448


title: WAU314


title: WAU313


title: DUK434


title: DUK420


title: DUK437


title: WAU315


title: DUK422


title: DUK416


title: DUK436


title: DUK418


title: DUK425


title: WAU308


title: DUK459


title: WAU306


title: DUK433


title: DUK419


title: DUK460


title: DUK430


title: DUK435


title: DUK404


title: DUK444


title: WAU301


title: DUK458


title: DUK471


title: DUK402


title: DUK468


title: DUK410


title: DUK452


title: DUK467


title: DUK417


title: DUK423


title: DUK485


title: DUK413


title: DUK409


title: DUK469


title: DUK408


title: BWH265


title: DUK412


title: DUK487


title: DUK443


title: UM114


title: DUK480


title: DUK466


title: BWH269


title: DUK456


title: DUK474


title: DUK488


title: BWH266


title: DUK484


title: DUK473


title: DUK465


title: DUK489


title: DUK411


title: BWH263


title: DUK478


title: DUK457


title: UM149


title: DUK475


title: BWH264


title: BWH257


title: WAU318


title: WAU379


title: DUK483


title: UM111


title: WAU332


title: BWH258


title: WAU320


title: BWH256


title: BWH255


title: BWH262


title: BWH254


title: WAU387


title: WAU363


title: BWH261


title: BWH260


title: DUK490


title: DUK479


title: BWH259


title: UCD038


title: UCD051


title: BWH243


title: UCD045


title: BWH239


title: BWH247


title: BWH248


title: BWH249


title: UCD039


title: PMH550


title: UCD050


title: UCD049


title: UCD054


title: BWH253


title: UCD053


title: PMH552


title: PMH551


title: BWH246


title: BWH230


title: PMH548


title: BWH213


title: PMH549


title: BWH234


title: BWH233


title: BWH235


title: PMH556


title: BWH226


title: BWH229


title: BWH224


title: PMH553


title: PMH555


title: BWH222


title: BWH225


title: UM132


title: UCD029


title: UCD006


title: UCD003


title: BWH211


title: BWH219


title: BWH210


title: UCD016


title: UCD021


title: UCD010


title: BWH208


title: BWH209


title: UM138


title: PMH528


title: BWH214


title: DUK428


title: DUK453


title: DUK442


title: Control7

status: Public on Aug 16 2020

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 control patient
ExVivo_Blood_Control

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, control patient

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 in the first 24h following clinical diagnosis of septic shock and non-septic shock.

value: control patient

value: whole blood

tag: gender

value: male


title: Control6


title: Control3

value: female


title: Control15


title: Control13


title: Control10


title: Control8


title: Control2


title: REA1565_SNS

description:
Gene expression of peripheral blood from non-septic shock patient
ExVivo_Blood_SNS

source_name: Peripheral Blood, non-septic shock

value: non-septic shock


title: Control4


title: Control14


title: Control1


title: SS_65exp2

description:
Gene expression of peripheral blood from septic shock patient
ExVivo_Blood_SS

source_name: Peripheral Blood, septic shock

value: septic shock


title: SS_14exp2


title: Control11


title: SS_116exp1


title: SS_73exp2


title: REA17427_SNS


title: Control12


title: Control5


title: Control9


title: SS_105exp1


title: REA17267_SNS


title: REA17443_SNS


title: SS_77exp1


title: REA17337_SNS


title: REA16236_SNS


title: REA15133_SNS


title: REA16217_SNS


title: REA17425


title: REA1566_SS


title: REA1567_SNS


title: REA17432


title: SS_124exp1


title: SS_80exp2


title: SS_138exp1


title: SS_135exp1


title: SS_84exp2


title: SS_47exp2


title: SS_76exp1


title: SS_101exp1


title: SS_24exp2


title: SS_130exp1


title: SS_56exp1


title: SNS_129_expI


title: SNS_103_expI


title: REA16219_SNS


title: SS_64exp1


title: SS_25exp2


title: SNS_117_expI


title: SNS_128_expI


title: SS_94exp2


title: SS_121exp1


title: SS_91exp1


title: SIRS_32exp1


title: SS_137exp1


title: SIRS_26exp1


title: SS_4exp1


title: SS_12exp1


title: SS_6exp1


title: SS_9exp1


title: SNS_127_expI


title: SS_47exp1


title: REA16260_SNS


title: SS_44exp1


title: SNS_115_expI


title: SIRS_33exp1


title: SS_77exp2


title: REA1521_SS


title: REA159_SS


title: SS_24exp1


title: REA1555_SS


title: SS_151exp1


title: SS_85exp1


title: REA17435


title: REA1542_SS


title: SS_89exp2


title: SS_61exp2


title: SS_20exp2


title: REA16251_SS


title: SS_81exp2


title: REA17294_SNS


title: REA16207_SS


title: REA15154_SS


title: REA1512_SS


title: SNS_106_expI


title: SS_14exp1


title: SS_80exp1


title: SL_42expII


title: SS_17exp2


title: REA16254_SNS


title: SS_143exp1


title: SS_142exp1


title: REA16243_SNS


title: REA17415


title: REA17277


title: SS_40exp1


title: SS_56exp2


title: SS_50exp2


title: SS_87exp1


title: SS_92exp2


title: SS_1exp2


title: SIRS_74exp2


title: REA16248_SS


title: REA15161_SS


title: REA16168_SS


title: SS_23exp2


title: SNS_55_expI


title: SL_160expI


title: REA15153_SS


title: REA17422_SNS


title: Wilms' tumor primary culture CF-00333

status: Public on Aug 12 2020

city: Beaverton

first: Charles

last: Keller

state: Oregon

address: 12655 Sw Beaverdam Rd West

department: Pediatric Cancer Biology

institute: cc-TDI

data_processing:
raw reads aligned to GRCh38 human reference genome using STAR
aligned transcripts were quantified using RSEM
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: result files are In tabular format. These files have quantified TPM data with additional information

source_name: tumor cells

extract_protocol:
Total RNA was extracted at BGI and analyzed on a Agilent 2100.
Library was constructed using the BGISeq-500 Transcriptome library construction protocol: 1. Calculate the DNA input and prepare the library adapters. 2. End-repair step following Carøe et al. 2017 with the addition of 1 μl "Reaction enhancer" consisting of 25% Poly-Ethylene Glycol (PEG4000); 2 μg/μL Bovine Serum Albumin (BSA) and 400 mM NaCl. 3. Ligation step following Carøe et al. 2017 by using 1 μl 10 μM BGISeq-500 adapters. 4. Fill-in step of the adapter to complete library building and purification using 1:5 volume of PB binding buffer (Qiagen) and using Monarch DNA Cleanup Columns (New England Biolabs, Massachusetts, USA). 5. Wash with 750 µl buffer PE (Qiagen). 6. Incubate for 5 minutes at 37 °C. 7. Elute in 40 µl buffer EB (Qiagen). 8. To determine the number of cycles used in index PCR, performe a qPCR in a 20 µl reaction volume using 1:20 dilution of: purified library template, 0.2 mM dNTPs (Invitrogen), 0.04 U/µl AmpliTaq Gold DNA polymerase (Applied Biosystems, Foster City, California, USA), 2.5 mM MgCl2 (Applied Biosystems), 1X GeneAmp, 10X PCR Buffer II (Applied Biosystems), 1 µl SYBR Green (Invitrogen, Carlsbad, California, USA), 0.2 µM forward and reverse primers mixture(CommonprimerBGI forward primer and one of the indexed reverse primers), 13.48 µl AccuGene molecular biology water (Lonza)

value: tumor cells

value: Wilms' tumor primary culture CF-00333


title: SS_5exp1


title: Ras/Src HSD rep4

status: Public on Jul 28 2020

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Trim Galore (v0.4.4) was applied for trimming adapter and low quality reads
Trimmed reads were mapped to dm3 whole genome using tophat2 (2.0.11) with parameters --library-type fr-firststrand -p 8
Gene annotations were obtained from Ensembl Drosophila genome (dm3). Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: dm3
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

organism: Drosophila melanogaster

source_name: tumor

growth_protocol: Cultures were carried out on Bloomington semi-defined medium (https://bdsc.indiana.edu/information/recipes/germanfood.html) and contained sucrose (0.15 M and 1.0 M in CD and HSD, respectively) as the only purified sugar source. Ingredients were obtained from; Agar (Fisher Scientific; BP2641-1), Brewer’s Yeast (MP Biomedicals; 903312, Lot: BCBN0171V), Yeast Extract (Sigma-Aldrich; 70161), Peptone (Sigma-Aldrich; 82303), Sucrose (Fisher Scientific; S/8560/63), Magnesium sulfate hexahydrate (Fluka; 00627), Calcium chloride dihydrate (Sigma-Aldrich; 223506), Propionic acid (Sigma-Aldrich; P1386), p-Hydroxy-benzoic acid methyl ester (Sigma-Aldrich; H5501). Larvae were raised up until the indicated time point after egg laying at which point the relvant tissue was dissected.

extract_protocol:
RNA from pooled dissected tissue was extracted with the QIAGEN RNeasy Mini Kit.
RNA-seq libraries were prepared from a minimum of 10ng of total RNA using the Illumina Truseq mRNA stranded library prep kit (Illumina, San Diego, USA) according to the manufacturer’s protocol.  Library quality was checked on a Bioanalyser HS DNA chip and concentrations were estimated by Qubit measurement.
Libraries were pooled in equimolar quantities and sequenced on a Hiseq2500 using paired end 100bp reads. At least 35 million reads passing filter were achieved per sample.

treatment_protocol: Na.

value: tumor

value: day 14

value: larval eye disc


title: Ras/Src HSD rep2


title: Ras/Src CD rep4 [tumor]

value: day 8


title: SNS_125_expI


title: SS_93exp2


title: REA1573_SS


title: SS_57exp2


title: REA16258_SS


title: Ras/Src CD rep3 [tumor]


title: Ras/Src HSD Late rep4

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
Sequenced reads were mapped to dm3 whole genome using tophat2 (2.0.11) with parameters --library-type fr-firststrand -p 8
Gene annotations were obtained from Ensembl Drosophila genome (dm3). Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: dm3
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

source_name: body wall muscle

value: day 16

tag: tumor-type

value: Ras/Src HSD

value: body wall muscle


title: Ras/Src CD rep1 [tumor]


title: Ras/Src HSD Late rep3


title: SNS_1_expI


title: REA17264


title: SS_43exp2


title: SS_39esp2


title: SS_100exp1


title: SS_69exp2


title: Ras/Src HSD rep1


title: Ras/Src CD rep2 [tumor]


title: REA16165_SS


title: SNS_50_expI


title: SNS_46_expI


title: Ras/Src HSD Mid rep4


title: Ras/Src HSD Mid rep3


title: Ras/Src HSD Mid rep2


title: Ras/Src HSD Late rep2


title: Ras/Src HSD Early rep4

value: day 12


title: Ras/Src HSD Early rep2


title: Ras/Src HSD Mid rep1


title: Ras/Src HSD Early rep1


title: Ras/Src HSD Early rep3


title: Ras/Src CD rep4

value: Ras/Src CD


title: SNS_134_expI


title: REA16238_SNS


title: Ras/Src CD rep2


title: Ras/Src HSD Late rep1


title: Ras/Src CD rep1


title: Ras/Src CD rep3


title: GM02640

status: Public on Jul 20 2020

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

institute: IIT Gandhinagar

data_processing:
Unpaired sequencing reads were trimmed and subjected to proprietary quality filtration for the Ion Torrent platform (minimum quality threshold 20).
Reads were mapped using Bowtie2 (with default options) against repeat-unmasked (hg38.fa) human genome. Reads were mapped end-to-end with default option.
Mapped reads were subjected to variant calling across the sequenced locations in all datasets using BCFtools. A minimum coverage of 5 reads was used as a threshold to filter the variants.
Genome_build: hg38

growth_protocol: HEK293T and human fibroblasts cells were grown in DMEM supplemented with 10 % FBS at 37˚C and 5% CO2.

extract_protocol:
DNA isolated from HEK293T and GM02639 cells were sonicated. The lysates were clarified and subjected to MeDIP by anti-5-methylcytosine antibody cocktail. MeDIP DNA was purified using PCR cleanup kit. Genomic DNA was isolated from GM02640 and GM02641 cells.
The Ion Xpress(TM) Plus Fragment Library Kit (Cat. no. 4471269) was used for library preparation. All the steps were performed as per manufacturer’s instructions for sequencing on Ion Torrent S5 platform without any barcoding.

treatment_protocol: HEK293T cells were transduced with following shRNA lentiviruses: non-targeting (CT), CGGBP1-targeting (KD). For stable transduction, control- and CGGBP1-shmiR transduced cells were selected with 10 ug/ml puromycin for a week. GM02639 cells were transfected twice with following siRNA: non-targeting (CT) and CGGBP1-targeting (KD). Genomic DNA was isolated from GM02640 and GM02641 cells without any treatment.

tag: cell line


title: GM02641


title: klf_atac-seq_klf4_klf5_b

status: Public on Jul 14 2020

city: Saint Louis

first: Kitra

last: Cates

state: MO

address: 4523 Clayton Ave, MCD SCI 361

department: Developmental Biology

institute: Washington University in St. Louis

data_processing:
At least 45 million omni-ATAC reads per sample were processed by Atac-seq Integrative Analysis Pipeline (AIAP, https://github.com/Zhang-lab/ATAC-seq_QC_analysis).
AIAP trims adapters using Cutadapt
AIAP aligns fragments using BWA-MEM to the hg38 human reference genome
AIAP removes low quality reads using methylQA
AIAP normalizes count signal by 10 million input single end reads
AIAP call peaks by macs2 with q-value less than 0.01
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files of biological replicates for ATAC-seq experiments

source_name: Dermal fibroblasts

growth_protocol: Direct neuronal reprogramming of human fibroblasts to neurons was performed as previously described (Abernathy et al., 2017; Richner et al., 2015).

extract_protocol: Omni-ATAC-seq preparation was performed as outlined in Corces et al. (Corces et al., 2017)

value: Coriell GM02171

tag: overexpression 1

tag: overexpression 2

value: KLF4, KLF5


title: GM02639_CT

tag: antibody

value: MABE146 and SAB2702243 (Sigma) ; NBP2-42813 (Novus Biologicals)

tag: sirna

value: non-targeting RNAi


title: iPSC

status: Public on Jul 16 2020

city: Baltimore

first: Xitiz

last: Chamling

state: MD

address: 400 N. Broadway

institute: Johns Hopkins University School of Medicine

description: single cell from 10X

data_processing:
Cell Ranger 2.1.0 pipeline was used to generate count matrices according to manufacturer recommendations
Genome_build: hg19
Supplementary_files_format_and_content: 10x filtered feature-barcode matrix where rows and columns are barcodes and genes. Created by running cellranger mat2csv on filtered_gene_bc_matrices_h5.h5

source_name: iPSC derived PDGFRa+ cells

growth_protocol: Cryopreserved PBMCs were reprogrammed to iPSCs via transduction of episomal vectors containing Oct3/4, Sox2, Klf4 c-Myc, and Bcl-xl. iPSCs were differentiated to OPCs using protocol described in PMID 26134954. 60 days after initiation of differentiation, cells were detached from plate with TrypLE, labeled with anti-PDGFRa antibody, and FACS sorted on PDGFRa positivity. Sorted cells were then replated for an additional 6 days prior to collection.

extract_protocol:
Cells were detached with TrypLE treatment, washed, filtered to remove aggregates, then captured on 10x Genomics platform for single cell RNA seq
10x Genomics Single Cell 3' v2 according to Manufacturers Recommendation

value: iPSCs

value: Day 66


title: GM02639_KD

value: CGGBP1 knocked-down by RNAi


title: klf_atac-seq_klf4_klf5_a


title: rn7sk_atac-seq_sh7sk_a


title: rn7sk_atac-seq_sh7sk_b


title: klf_atac-seq_luc_b

value: luciferase


title: rn7sk_atac-seq_shctrl_b

value: shCTRL


title: klf_atac-seq_klf5_b


title: fibro_fate_erasure_atac-seq_i1l3_b

data_processing:
At least 45 million omni-ATAC reads per sample were processed by Atac-seq Integrative Analysis Pipeline (AIAP, https://github.com/Zhang-lab/ATAC-seq_QC_analysis).
AIAP trims adapters using Cutadapt
AIAP aligns fragments using BWA-MEM to the hg38 human reference genome
AIAP removes low quality reads using methylQA
AIAP normalizes count signal by 10 million input single end reads
AIAP call peaks by macs2 with q-value less than 0.01
Bam files were used as input into bedtools genomeCoverageBed and converted to BedGraph format. Then, the BedGraph files were converted to bigwig format (.bw) by bedGraphToBigWig.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files of biological replicates for ATAC-seq experiments

value: ISL1, LHX3


title: fibro_fate_erasure_atac-seq_i1l3_a


title: rn7sk_atac-seq_shctrl_a


title: klf_atac-seq_klf5_a


title: rn7sk_atac-seq_fibro_a


title: klf_atac-seq_klf4_b


title: klf_atac-seq_klf4_a


title: rn7sk_atac-seq_fibro_b


title: fibro_fate_erasure_atac-seq_myt1l_a


title: fibro_fate_erasure_atac-seq_myt1l_b


title: klf_atac-seq_luc_a


title: fibro_fate_erasure_rna-seq_i1l3_a

data_processing:
Sequencing reads were mapped to the human reference genome (GRCh38) using STAR (Dobin and Gingeras, 2015).
Raw gene counts were derived by deepTools multiBamSummary with the option –outRawCounts (Ramírez et al., 2016).
To account for technical variations, the raw gene counts were normalized using the RUVSeq (Remove Unwanted Variation (v1.20.0) (Risso et al., 2014)) based on the factor analysis of replicate samples.
Differential expression analysis was performed using DESeq2 (v1.26.0) (Love et al., 2014).
Bam files were used as input into bedtools genomeCoverageBed and converted to BedGraph format. Then, the BedGraph files were converted to bigwig format (.bw) by bedGraphToBigWig.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files of biological replicates for RNA-seq experiments

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using the RNeasy plus micro kit (QIAGEN, USA) as instructed by the manufacturer.
mRNA was prepared for Illumina sequencing using poly-A library preparation.


title: fibro_fate_erasure_atac-seq_mir_b


title: fibro_fate_erasure_atac-seq_fibro_b


title: fibro_fate_erasure_rna-seq_mir_b


title: fibro_fate_erasure_atac-seq_mir_a


title: fibro_fate_erasure_rna-seq_myt1l_b


title: fibro_fate_erasure_rna-seq_fibro_b


title: fibro_fate_erasure_rna-seq_i1l3_b


title: fibro_fate_erasure_rna-seq_mir_a


title: fibro_fate_erasure_rna-seq_fibro_a


title: rn7sk_rna-seq_sh7sk_b

data_processing:
Raw reads were aligned to human reference genome (GRCh38) by STAR (Dobin and Gingeras, 2015).
Gene counts were derived from the number of uniquely aligned reads by Subread:featureCounts (Liao et al., 2014).
Counts were normalized by trimmed mean of M-values (TMM) using edgeR (Robinson et al., 2010).
EdgeR (v3.11; Robinson et al., 2010; McCarthy, Chen, and Smyth, 2012) and limma (Ritchie et al., 2015) were used to identify differentially expressed genes.
Bigwig files were generated using deepTools bamCoverage feature (Ramírez et al., 2016).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files of biological replicates for RNA-seq experiments

extract_protocol:
Total RNA was extracted using the RNeasy plus micro kit (QIAGEN, USA) as instructed by the manufacturer.
SMARTer Ultra Low Input RNA Kit (Clontech, USA)


title: rn7sk_rna-seq_shctrl_a


title: rn7sk_rna-seq_fibro_b


title: miR_only_scRNA-seq_D20

description: Single cell RNA

data_processing:
Raw 10x reads were processed with the Cell Ranger count pipeline using default parameters (Cell ranger v3.1.0, 10x Genomics).
Reads were aligned to the hg38 reference index provided by 10x Genomics (refdata-cellranger-GRCh38 v3.0.0).
Cell barcode and UMI (unique molecular identifier) were extracted and corrected from the feature library using the same methods as gene expression read processing.  Feature-barcode matrices were generated by counting distinct UMIs of each gene within a given individual cell (Zheng et al., 2017).
Using the R package Seurat (v3.1.4) (Satija et al., 2015), we removed cells where features less than 200 are detected and mitochondrial counts are high, then filtered features detected in cells less than 10, and removed unwanted variation from the gene expression by regressing out proportion of mitochondrial UMIs and overall UMIs.
Genome_build: hg38
Supplementary_files_format_and_content: Barcodes detected, genes detected and matrix files are provided for each sample.

extract_protocol:
Reprogramming times (Day 0, 5, 10, 15, and 20) were stacked so that cells at different time points of neuronal conversion could be collected on the same day. Cells were washed with sterile PBS, detached using Trypsin, and collected by centrifugation in 10% FBS in DMEM. Cells were washed using BSA in PBS by gentle pipetting. Collection and wash steps were repeated once, then cells were counted on a hemocytometer and volume was adjusted to achieve 1,000 cells/µL with 10% FBS in DMEM. Cells were placed on ice to be immediately proceeded with 10X Genomics Single Cell processing.
For single-cell library preparation, we used the 10x Genomics platform with the Chromium Single Cell 3′ Reagents Kits according to manufacturer instructions. cDNA libraries were quantified on an Agilent BioAnalyzer. These libraries were sequenced on a NovaSeq S4.

tag: reprogramming time


title: miR_only_scRNA-seq_D10

description: Single cell RNA


title: miR_I1L3_scRNA-seq_D20

description: Single cell RNA

extract_protocol:
At Day 0, 5, 10, 15 and 20 days into reprogramming, cells were washed with sterile PBS, detached using Trypsin, and collected by centrifugation in complete neuronal media supplemented with 5% FBS. Cells were counted using a hemocytometer and were resuspended in Cryostar CS10 cryopreservation medium at a concentration of 100 cells per μL. These aliquots were placed in a cryogenic freezing container and stored at -80°C until all timepoints were collected (Figure 1).
For single-cell library preparation, we used the 10x Genomics platform with the Chromium Single Cell 3′ Reagents Kits according to manufacturer instructions. cDNA libraries were quantified on an Agilent BioAnalyzer. This timecourse single cell preparation was sequenced on an Illumina HiSeq 2500.


title: miR_only_scRNA-seq_D5

description: Single cell RNA


title: rn7sk_rna-seq_fibro_a


title: miR_I1L3_scRNA-seq_D15_1

description: Single cell RNA


title: miR_only_scRNA-seq_D0

description: Single cell RNA


title: miR_I1L3_scRNA-seq_D15_2

description: Single cell RNA

extract_protocol:
Reprogramming times (Day 10, 12.5, and 15) were stacked so that cells at different time points of neuronal conversion could be collected on the same day. Cells were washed with sterile PBS, detached using Trypsin, and collected by centrifugation in 10% FBS in DMEM. Cells were washed using BSA in PBS by gentle pipetting. Collection and wash steps were repeated once, then cells were counted on a hemocytometer and volume was adjusted to achieve 1,000 cells/µL with 10% FBS in DMEM. Cells were placed on ice to be immediately proceeded with 10X Genomics Single Cell processing.
For single-cell library preparation, we used the 10x Genomics platform with the Chromium Single Cell 3′ Reagents Kits according to manufacturer instructions. cDNA libraries were quantified on an Agilent BioAnalyzer. These libraries were sequenced on a NovaSeq S4.


title: miR_only_scRNA-seq_D15

description: Single cell RNA


title: fibro_fate_erasure_rna-seq_myt1l_a


title: miR_I1L3_scRNA-seq_D10_1

description: Single cell RNA


title: miR_I1L3_scRNA-seq_D12.5

description: Single cell RNA


title: fibro_fate_erasure_atac-seq_fibro_a


title: miR_I1L3_scRNA-seq_D10_2

description: Single cell RNA


title: miR_I1L3_scRNA-seq_D5

description: Single cell RNA


title: miR_I1L3_scRNA-seq_D0

description: Single cell RNA


title: MERFF-95-S108

status: Public on Jul 13 2020

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

description: Derived from patient with pathogenic m.8344A>G mutation

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools for reads uniquely mapping to the nuclear genome.
Reads were subsequently filtered for alignment quality of >Q20 and were required to be properly paired. We used MACS2 to call all  ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues.
For all subsequent analysis we discarded peaks falling within these regions. Mitochondrial genotypes were inferred for each ATAC-seq sample using a custom python script after removing PCR duplicates
Genome_build: hg19
Supplementary_files_format_and_content: Heteroplasmy TSV showing per-sample (single-cell) values at m.8344

source_name: Coriell cell line

growth_protocol: RPMI, 15%FBS, Pen/Strep

extract_protocol:
NP40 lysis
Single cell ATAC-seq (C1 Fluidigm)

value: lymphoblastoid cell line


title: MERFF-96-S109


title: MERFF-94-S107


title: MERFF-93-S106


title: rn7sk_rna-seq_sh7sk_a


title: MERFF-92-S105


title: rn7sk_rna-seq_shctrl_b


title: MERFF-90-S103


title: MERFF-8-S21


title: MERFF-89-S102


title: MERFF-86-S99


title: MERFF-85-S98


title: MERFF-88-S101


title: MERFF-83-S96


title: MERFF-84-S97


title: MERFF-81-S94


title: MERFF-82-S95


title: MERFF-79-S92


title: MERFF-77-S90


title: MERFF-80-S93


title: MERFF-75-S88


title: MERFF-74-S87


title: MERFF-72-S85


title: MERFF-91-S104


title: MERFF-70-S83


title: MERFF-69-S82


title: MERFF-73-S86


title: MERFF-6-S19


title: MERFF-68-S81


title: MERFF-9-S22


title: MERFF-7-S20


title: MERFF-67-S80


title: MERFF-66-S79


title: MERFF-87-S100


title: MERFF-71-S84


title: MERFF-61-S74


title: MERFF-64-S77


title: MERFF-60-S73


title: MERFF-78-S91


title: MERFF-76-S89


title: MERFF-5-S18


title: MERFF-63-S76


title: MERFF-57-S70


title: MERFF-59-S72


title: MERFF-58-S71


title: MERFF-56-S69


title: MERFF-54-S67


title: MERFF-55-S68


title: MERFF-52-S65


title: MERFF-50-S63


title: MERFF-53-S66


title: MERFF-4-S17


title: MERFF-49-S62


title: MERFF-48-S61


title: MERFF-46-S59


title: MERFF-47-S60


title: MERFF-65-S78


title: MERFF-45-S58


title: MERFF-43-S56


title: MERFF-44-S57


title: MERFF-62-S75


title: MERFF-41-S54


title: MERFF-3-S16


title: MERFF-38-S51


title: MERFF-40-S53


title: MERFF-37-S50


title: MERFF-39-S52


title: Ras/Src HSD rep3

tag: tissue

value: tumor

value: day 14

value: larval eye disc


title: MERFF-36-S49


title: MERFF-33-S46


title: MERFF-34-S47


title: MERFF-32-S45


title: MERFF-51-S64


title: MERFF-31-S44


title: MERFF-35-S48


title: MERFF-30-S43


title: MERFF-2-S15


title: MERFF-27-S40


title: MERFF-42-S55


title: MERFF-23-S36


title: MERFF-22-S35


title: MERFF-26-S39


title: MERFF-24-S37


title: SNS_97_expI

value: non-septic shock

value: whole blood

value: female


title: MERFF-25-S38


title: MERFF-21-S34


title: MERFF-20-S33


title: MERFF-19-S32


title: MERFF-1-S14


title: MERFF-17-S30


title: MERFF-18-S31


title: MERFF-15-S28


title: MERFF-14-S27


title: MERFF-16-S29


title: MERFF-28-S41


title: MERFF-13-S26


title: MERFF-11-S24


title: mtscATACseq2

data_processing:
Fastqs were demultiplexed usiing CellRanger-ATAC mkfastq (v1.0.0)
Sequencing reads were aligned to a modified hg19 reference using CellRanger-ATAC count (v1.0.0). Single-cells were called using the default parameters from this step.
Genome_build: hg19
Supplementary_files_format_and_content: Processed fragment files from 10x CellRanger-ATAC count

source_name: Cell line mix TF1 and GM11906

growth_protocol: RPMI, 10%FBS, Pen/Strep, 2ng/ml GM-CSF for TF1 cells; RPMI, 15%FBS, Pen/Strep for GM11906 cells

extract_protocol:
Various lysis conditions as indicated above
Custom 10x Genomics scATAC-seq (mtscATAC-seq)

value: Cell line mix TF1 and GM11906

tag: lysis

tag: decrosslinking

value: 6h at 60C before PCR

tag: fixation

value: 1% FA

tag: wash

value: No tween wash


title: mtscATACseq1

value: 1h at 60C before PCR


title: MERFF-10-S23

tag: cell type


title: ConditionE

value: 10x protocol (Omni-ATAC)

value: 12h at 60C before PCR

value: Tween wash


title: ConditionD


title: ConditionC


title: MERFF-29-S42


title: MERFF-12-S25


title: ConditionB


title: KI-1_S7

status: Public on Jul 09 2020

city: BETHESDA

first: RAJAKUMAR

last: ANBAZHAGAN

address: 49 CONVENT DRIVE, NIH

department: NICHD, DDB

institute: NICHD, NIH

description: GRTH Knock-In CB-1

data_processing:
PartekFlow software was used for read QA/QC report
The sequenced reads were trimmed to remove the adapters
STAR method was used to align the RNA-seq reads with mouse mm10 reference genome
The quantification of transcriptome abundance was performed using Partek E/M algorithm in PartekFlow software.
Differentially expressed genes (DEGs) between WT and KI gentotypes were generated with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files contains results from DESeq2 which includes fold change calculations between KI vs WT along with geneName, total count, p-value, FDR stepup etc.

organism: Mus musculus

source_name: CB in germ cells of GRTH Knock-In

extract_protocol:
Chromatoid bodies isolated from Germ cells of Testis was used to prepare RNA using Phenol:Chloroform:Isoamylalcohol (25:24:1). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Germ cells were fixed in 0.1% Formaldehyde, prior to isolation of chromatoid bodies

tag: strain background

tag: genotype/variation

value: GRTH-KI (R242H)

value: Testis

value: Germ Cells

tag: organelle

value: Chromatoid body (CB)


title: KI-2_S8

description: GRTH Knock-In CB-2


title: ConditionA

value: regular PCR


title: WT-3_S3

description: Wild Type CB-3

source_name: CB in germ cells of WT

value: WT


title: KI-5_S11

description: GRTH Knock-In CB-4


title: WT-6_S6

description: Wild Type CB-5


title: WT-4_S4

description: Wild Type CB-4


title: WT-2_S2

description: Wild Type CB-2