title: CBMS1_Day3Diff_ESC_single_35perS_08

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_35perS_06

status: Public on Jun 20 2020

type: SRA

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description: 80kb resolution data

library_source: genomic

data_processing:
Sequence reads were trimmed to remove adapter sequences using the cutadapt program before mapping. For WGA samples, we performed a two-step adapter trimming, first removing the Illumina adapter based on the index of each NGS library and then removing the SEQXE adapter. As the SEQXE adapter sequence was not available, we empirically estimated it as the sequence that repeatedly appeared near the 5’ end.
Trimmed reads were mapped into mm9 and CBMS1-specific (CBA/MsM) diploid genome based on mm9 genomeby using bwa (ver: 0.7.10-r789, command: bwa aln => bwa samse). CBMS1-specific diploid genome was constructed as described in Sakata et al. Development (2017) with minor modifications using CBA or MsM strain genomic reads. Duplicated reads mapped into mm9 were removed by using picard tool and the reads overlapped with mm9 black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered out. The mapped reads with MAQP>10 were used for the further analysis. For the diploid genome mapping, we defined MAPQ>16 as the allele specific reads and used the liftover tool (UCSC Genome Browser) to convert to the mm9 genome coordinates. After this, duplicate reads identified as an identical chromosome start position and strand information were filtered out.
Single-cell data (CBMS1, differentiated CBMS1, EpiSC un-resolved at 80-kb): first, we counted the reads in non-overlapping 80-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the merged G1 control. Binarization was performed using the Mappability corrected 25per-S (25% S-phase) , Mid-S (50% S-phase), 75per-S (75% S-phase) reads described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy"; options for Mid-S, 75per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"; 1-somy, unreplicated; 2-somy, replicated]. In the processed data files, replicated bin was shown as 1, unrelicated bin was shown as -1, and no-data was shown as 0. “Repliscore” was calculated as a percentage of replicated bins in the total number of replicated and unreplicated bins.
Single-cell haplotype-resolved chrX data (d0, d2, d7): after the specific filtering steps for haplotype-resolved data, we counted the reads in non-overlapping 400-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the filtered merged G1 control. Binarization was performed as described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy" ; options for Mid-S, 75per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"].
For paired-end reads, only "R1" (Fwd) reads were used for the analysis.
Binarized 40kb data: Sample_Name_40k_100S_MAP_2HMM2_eps0.01.binary.bedGraph
Genome_build: mm9
Supplementary_files_format_and_content:  We provide three types of processed data files. One is the binarized data (scRepliseq_data_884cells_G1_Sphase_binary_data_80kb.txt). Second is the sample information data (scRepliseq_data_sample_Info.txt). Third is the haplotype-resolved Mid-S binarized data of chrX (scRepliseq_d0_33_CBA_XX_chrX_only_400kb.txt, scRepliseq_d0_33_MsM_XX_chrX_only_400kb.txt, scRepliseq_d2_27_CBA_XX_chrX_only_400kb.txt, scRepliseq_d2_27_MsM_XX_chrX_only_400kb.txt, scRepliseq_d7_36_XX_Xa_chrX_only_400kb.txt, scRepliseq_d7_36_XX_Xi_chrX_only_400kb.txt). We also provide README file for the description of each processed file.
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

organism: Mus musculus

source_name: Day3 Differentiated CBMS1 ESC

growth_protocol: CBMS1 mESCs have been described (Murakami et al. Development, 2011) and were grown in 2i/LIF medium as described (Hayashi K et al., Nat. Protoc., 2013). EpiSCs (female) and their culture protocol have been described and were grown in Activin/FGF medium as described (Tesar et al. 2007).

extract_protocol:
For single cells samples, cells were sorted with a Sony SH800 cell sorter using the single-cell mode. Sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a SeqPlex kit (Sigma, SEQXE). Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu).
NGS libraries were constructed with a NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions, with slight modifications based on the previous study (Kadota et al., Sci. Rep. 2017). For a multi-plex NGS run, a SeqCap adapter kit A/B (Roche, 07141530001/ 07141548001) and NEXTflex DNA barcode (Bio Scientific, NOVA) were used. The samples were subjected to NGS on an Illumina Hiseq 1500 system (80-bp length, single-read).

treatment_protocol: For differentiation, CBMS1 mESCs were differentiated to EpiLCs for 2 days and then switched to aggregation culture (EB/embryoid body culture) in Nunclon Sphera 96U-well plates (ThermoFisher, #174925), starting from 2,000 EpiLCs per well exactly as described (Hayashi K et al. Nat. Protoc., 2013), except for the use of plain GK15 medium (Hayashi K et al. Nat. Protoc., 2013) without any additional factors added during the aggregation culture. This process is practically identical to the SFEBq neural method of mESC differentiation (serum-free floating culture of EB-like aggregates with quick reaggregation) (Eiraku et al. Nat. Protoc., 2012) except that we started from EpiLCs instead of mESCs. In our hands, this resulted in efficient formation of neurectoderm cells based on gene expression after 7 days of differentiation (2 days to EpiLCs and then 5 additional days of EB culture).

tag: strain

value: CBA/MsM

tag: cell type

value: day3 differentiated ESCs

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

value: FALSE

tag: cell cycle phase


title: CBMS1_Day3Diff_ESC_single_35perS_07

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_35perS_05

description: 80kb resolution data


title: M14

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

country: China

institute: Tongji university

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to GRCm38.84 whole genome using tophat2
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Read count and FPKM ( Fragments Per Kilobase Million) for each Sample

molecule: total RNA

source_name: hindlimb muscles

extract_protocol:
hindlimb muscles were washed with PBS, minced, and digested in  Ham's F10 Nutrient mix(Gibco) containing type II collagenase (2 mg/ml), dispase II(2.4U/ml), CaCl2(2.5mM,Sigma) for 1 hr at 37°C.Digested tissue was successively filtered through 70-μm and 40-μm cell strainers (BD Biosciences) and then centrifuged with 500g for 5min. The cell pellet was resuspended with PBS. Tomato+ cells were sorted by Bio-Rad S3e and then single cells were picked with fluorescence microscope.
Libraries were prepared according to Nextera® XT DNA Library Prep Kit for Illumina  (Cat# FC-131-1096)

tag: tissue

value: hindlimb muscles

tag: age

value: adult

tag: genotype

tag: treatment

value: Injection of Tamoxifen 2mg/mice once a day for 3 days


title: CBMS1_Day3Diff_ESC_single_35perS_04

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_35perS_03

description: 80kb resolution data


title: M12


title: OCH-244  chronic hepatitis C

type: RNA

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

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

organism: Homo sapiens

source_name: liver tissue

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: Liver tissue was obtained by liver biopsy.

extract_protocol: Total RNA from liver biopsy was extracted commercially available kit (miReasy mini kit (Qiagen)).

treatment_protocol: Liver tissue sample was obtained before anti-viral treatment.

tag: disease state

value: chronic hepatitis C

tag: Sex

value: M

tag: bmi

tag: viral infection

value: HCV


title: CBMS1_Day3Diff_ESC_single_35perS_01

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_25perS_08

description: 80kb resolution data


title: M10


title: CBMS1_Day3Diff_ESC_single_25perS_07

description: 80kb resolution data

value: TRUE


title: CBMS1_Day3Diff_ESC_single_25perS_06

description: 80kb resolution data


title: M15


title: OCH-246  chronic hepatitis C

value: F


title: OCH-247  chronic hepatitis C


title: OCH-245  chronic hepatitis C


title: M11


title: CBMS1_Day3Diff_ESC_single_25perS_05

description: 80kb resolution data


title: OCH-242  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_25perS_03

description: 80kb resolution data


title: OCH-243  chronic hepatitis C


title: M9


title: M13


title: CBMS1_Day3Diff_ESC_single_25perS_04

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_25perS_02

description: 80kb resolution data


title: M7


title: OCH-241  chronic hepatitis C


title: CBMS1_Day3Diff_ESC_single_35perS_02

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_G1_06

description: 80kb resolution data

source_name: Day2 Differentiated CBMS1 ESC

value: day2 differentiated ESCs


title: CBMS1_Day2Diff_ESC_single_G1_05

description: 80kb resolution data


title: M8


title: OCH-240  chronic hepatitis C


title: M6


title: OCH-239  chronic hepatitis C


title: M5


title: CBMS1_Day2Diff_ESC_single_G1_02

description: 80kb resolution data


title: M4


title: OCH-238  chronic hepatitis C


title: OCH-237  chronic hepatitis C


title: CBMS1_Day2Diff_ESC_single_75perS_09

description: 80kb resolution data


title: M3


title: CBMS1_Day2Diff_ESC_single_75perS_08

description: 80kb resolution data


title: OCH-236  chronic hepatitis C


title: CBMS1_Day2Diff_ESC_single_75perS_06

description: 80kb resolution data


title: OCH-235  chronic hepatitis C


title: CBMS1_Day2Diff_ESC_single_G1_03

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_25perS_01

description: 80kb resolution data


title: M2


title: CBMS1_Day2Diff_ESC_single_75perS_04

description: 80kb resolution data


title: M1


title: OCH-234  chronic hepatitis C


title: CBMS1_Day2Diff_ESC_single_75perS_05

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_75perS_07

description: 80kb resolution data

value: XX


title: OCH-233  chronic hepatitis C


title: CBMS1_Day2Diff_ESC_single_75perS_03

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_75perS_02

description: 80kb resolution data


title: R39_UC7_Clark

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

country: USA

institute: University of Illinois

data_processing:
Standard Illumina pipeline including CASSAVA
Sequenced reads were aligned to 56,044 gene models, build Wm82.a2.v1 DNA soybean cDNA gene models determined by the Soybean Genome Project (Schmutz et al. 2010) using Bowtie (Langmead et al. 2009). Bowtie parameters allowed up to three mismatches and up to 25 alignments per read.
Reads per kilobase of gene model per million mapped reads (RPKM) were calculated according to Mortazavi et al. (2008).
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: Excel file includes RPKM values for Sample

organism: Glycine max

source_name: seed coat dissected from 100-200 mg immature seed

growth_protocol: Plants were grown in optimal greenhouse conditions. Tissues were harvested at stated mg fresh weight. Whole seeds were dissected by hand to separate seed coats.

extract_protocol:
Total RNA was extracted from freeze-dried tissues using phenol:chloroform and a lithium chloride precipitation (Gonzalez and Vodkin 2007). Sequencing was performed by the Keck Center (University of Illinois) using an Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: immature seed coat

tag: Stage


title: CBMS1_Day2Diff_ESC_single_G1_01

description: 80kb resolution data

tag: strain

tag: cell type


title: CBMS1_Day2Diff_ESC_single_75perS_10

description: 80kb resolution data

tag: sample state

tag: xx or xo chromosomes in single cell samples


title: CBMS1_Day2Diff_ESC_single_65perS_13

description: 80kb resolution data

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)


title: OCH-231  chronic hepatitis C


title: CBMS1_Day2Diff_ESC_single_65perS_12

description: 80kb resolution data

tag: repliscore of 40–70%

tag: cell cycle phase


title: CBMS1_Day2Diff_ESC_single_65perS_11

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_65perS_09

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_65perS_08

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_65perS_07

description: 80kb resolution data


title: 24-Lung-Inflammatory-DCs-KO

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Reads were demultiplexed to Illumina BaseSpace with FastQ version 1.0.0
Read were mapped to mm10 reference using the STAR aligner (v2.3.1s) via the BaseSpace RNAExpress App v1.0
Abundance estimation of raw read counts was performed with Htseq-count via the BaseSpace RNAExpress App v1.0
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: UCSC mm10 (mouse)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: HDM treated lung inflammatory DCs mTOR{delta}APC

extract_protocol:
Total RNA was purified using RNAeasy Micro Kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent 2100 Bioanalyzer (RNA integrity number (RIN) >8.5; Eukaryote Total RNA Pico Kit, Agilent, USA)
RNA libraries were prepared for sequencing using standard Clontech laboratory and Illumina NexteraXT protocols

treatment_protocol: HDM - house dust mite allergy treatment. Mice were anesthetized with Isoflurane, and vaccinated intranasally (i.n.) with 25µL house dust mite extract (HDM) (1mg/mL protein content, Greer Labs). Injections were performed thrice weekly and mice were analyzed after 18d.

tag: genotype/variation

value: mTOR {delta}APC

value: House dust-mite (HDM) treated d17

tag: tissue

value: Lung

value: inflammatory DCs


title: OCH-229  chronic hepatitis C

tag: age


title: 23-Lung-Inflammatory-DCs-WT

source_name: HDM treated lung inflammatory DCs WT

value: wild type; littermate

tag: treatment


title: OCH-230  chronic hepatitis C

tag: disease state

tag: Sex


title: OCH-232  chronic hepatitis C

tag: bmi

tag: viral infection


title: CBMS1_Day2Diff_ESC_single_65perS_06

description: 80kb resolution data

value: CBA/MsM

value: Single cell

value: FALSE


title: 25-Lung-Inflammatory-DCs-KO


title: OCH-228  chronic hepatitis C


title: OCH-227  chronic hepatitis C


title: 22-Lung-Inflammatory-DCs-WT


title: CBMS1_Day2Diff_ESC_single_65perS_04

description: 80kb resolution data


title: 21-Lung-Inflammatory-DCs-WT


title: 26-Lung-Inflammatory-DCs-KO


title: CBMS1_Day2Diff_ESC_single_75perS_01

description: 80kb resolution data


title: OCH-226  chronic hepatitis C


title: CBMS1_Day2Diff_ESC_single_65perS_03

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_65perS_02

description: 80kb resolution data


title: 20-Lung-steady-state-AM-KO

source_name: Lung Alveolar macrophage mTOR{delta}APC

value: Steady-state

value: Alveolar macrophage


title: CBMS1_Day2Diff_ESC_single_65perS_01

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_55perS_11

description: 80kb resolution data


title: OCH-224  chronic hepatitis C

value: chronic hepatitis C


title: 19-Lung-steady-state-AM-KO


title: CBMS1_Day2Diff_ESC_single_55perS_10

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_55perS_09

description: 80kb resolution data


title: 18-Lung-steady-state-AM-KO


title: 17-Lung-steady-state-AM-WT

source_name: Lung Alveolar macrophage WT


title: CBMS1_Day2Diff_ESC_single_65perS_05

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_55perS_06

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_55perS_08

description: 80kb resolution data


title: 15-Lung-steady-state-AM-WT


title: CBMS1_Day2Diff_ESC_single_55perS_05

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_55perS_04

description: 80kb resolution data


title: OCH-221  chronic hepatitis C

value: HCV


title: CBMS1_Day2Diff_ESC_single_55perS_07

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_65perS_10

description: 80kb resolution data


title: OCH-222  chronic hepatitis C

value: M


title: OCH-225  chronic hepatitis C


title: OCH-220  chronic hepatitis C

value: F


title: CBMS1_Day2Diff_ESC_single_55perS_03

description: 80kb resolution data

value: day2 differentiated ESCs


title: CBMS1_Day2Diff_ESC_single_55perS_02

description: 80kb resolution data


title: 16-Lung-steady-state-AM-WT


title: CBMS1_Day2Diff_ESC_single_55perS_01

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_45perS_10

description: 80kb resolution data

value: XX

value: TRUE


title: 14-Lung-steady-state-CD11b-KO

source_name: Lung CD11b DCs mTOR{delta}APC

value: mTOR {delta}APC

value: FACS purified CD11b+ DCs


title: 13-Lung-steady-state-CD11b-KO

value: Lung


title: OCH-219  chronic hepatitis C


title: CBMS1_Day2Diff_ESC_single_45perS_09

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_45perS_11

description: 80kb resolution data


title: CBMS1_Day3Diff_ESC_single_55perS_09

description: 80kb resolution data

value: day3 differentiated ESCs


title: OCH-223  chronic hepatitis C


title: CBMS1_Day2Diff_ESC_single_45perS_08

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_45perS_07

description: 80kb resolution data


title: 12-Lung-steady-state-CD11b-KO


title: 11-Lung-steady-state-CD11b-WT

source_name: Lung CD11b DCs WT

value: wild type; littermate


title: CBMS1_Day2Diff_ESC_single_45perS_05

description: 80kb resolution data

value: CBA/MsM


title: CBMS1_Day2Diff_ESC_single_45perS_04

description: 80kb resolution data

value: Single cell


title: CBMS1_Day2Diff_ESC_single_45perS_03

description: 80kb resolution data

value: FALSE


title: 10-Lung-steady-state-CD11b-WT

value: Steady-state


title: CBMS1_Day2Diff_ESC_single_45perS_02

description: 80kb resolution data


title: 9-Lung-steady-state-CD11b-WT


title: OCH-216  chronic hepatitis C


title: OCH-215  chronic hepatitis C


title: CBMS1_Day2Diff_ESC_single_35perS_12

description: 80kb resolution data


title: 8-Spleen-CD11b-KO

source_name: Spleen CD11b DCs mTOR{delta}APC

value: Spleen


title: OCH-213  chronic hepatitis C

value: chronic hepatitis C


title: OCH-218  chronic hepatitis C

value: HCV


title: CBMS1_Day2Diff_ESC_single_G1_04

description: 80kb resolution data


title: 7-Spleen-CD11b-KO


title: OCH-212  chronic hepatitis C

value: M


title: OCH-211  chronic hepatitis C

value: F


title: CBMS1_Day2Diff_ESC_single_35perS_09

description: 80kb resolution data

value: day2 differentiated ESCs


title: CBMS1_Day2Diff_ESC_single_35perS_10

description: 80kb resolution data

value: XX


title: 6-Spleen-CD11b-WT

source_name: Spleen CD11b DCs WT


title: CBMS1_Day2Diff_ESC_single_35perS_08

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_35perS_07

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_45perS_06

description: 80kb resolution data


title: 5-Spleen-CD11b-WT


title: OCH-217  chronic hepatitis C


title: CBMS1_Day2Diff_ESC_single_35perS_06

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_45perS_01

description: 80kb resolution data


title: OCH-210  chronic hepatitis C


title: OCH-214  chronic hepatitis C


title: 4-Spleen-CD8a-KO

source_name: Spleen CD8a DCs mTOR{delta}APC

value: FACS purified CD8a DCs


title: CBMS1_Day2Diff_ESC_single_35perS_05

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_35perS_03

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_35perS_02

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_35perS_11

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_35perS_01

description: 80kb resolution data


title: 3-Spleen-CD8a-KO

value: mTOR {delta}APC


title: 2-Spleen-CD8a-WT

source_name: Spleen CD8a DCs WT


title: CBMS1_Day2Diff_ESC_single_25perS_12

description: 80kb resolution data

value: TRUE


title: CBMS1_Day2Diff_ESC_single_25perS_11

description: 80kb resolution data


title: OCH-208  chronic hepatitis C


title: OCH-209  chronic hepatitis C


title: CBMS1_Day2Diff_ESC_single_25perS_10

description: 80kb resolution data


title: OCH-206  chronic hepatitis C


title: OCH-207  chronic hepatitis C


title: 1-Spleen-CD8a-WT


title: CBMS1_Day2Diff_ESC_single_25perS_08

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_25perS_09

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_25perS_07

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_25perS_06

description: 80kb resolution data


title: CBMS1_Day2Diff_ESC_single_25perS_05

description: 80kb resolution data


title: ADA2_3

city: San Diego

first: Rekha

last: Dhanwani

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

data_processing:
Reads were mapped against GRCh38 reference using bowtie2-2.1.0
Reads mapping to the reference genome are further run  through Repenrich2 subset script to get uniquely mapping reads and multimapper reads
Run the multimappers and uniquely mapped reads through Repenrich2 script with hg38_LTR element to get the LTR counts
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

source_name: Primary Human Umbilical Vein Endothelial Cells

growth_protocol: HUVECs (P3) were thawed, revived and cultured till they reached confluency (4-5 days). Once confluent, they were trypsinized and plated in 6-well plates for siRNA transfections.

extract_protocol:
RNA was extracted from 200,000 HUVEC cells using Zymo kit following manufacturers protocol and ~400 ng RNA was used for library construction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HUVECs were transfected with non targeting siRNA (labeled Control) and ADA2 siRNA (labeled ADA2) using transfection reagent Dharmafect 4 (Dharmacon). Media was changed after 24 hours and cells were maintained for another 48 hours. RNA was extracted after 72 hours of transfction.

value: Primary Endothelial cells

tag: gender

value: Male

tag: passage number

tag: knockdown

value: ADA2 siRNA


title: ADA2_2

tag: cell type


title: CBMS1_Day2Diff_ESC_single_25perS_04

description: 80kb resolution data

tag: strain

value: CBA/MsM

tag: sample state

tag: xx or xo chromosomes in single cell samples


title: ADA2_1


title: CBMS1_Day2Diff_ESC_single_35perS_04

description: 80kb resolution data

value: Single cell

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%


title: OCH-205  chronic hepatitis C


title: CBMS1_Day2Diff_ESC_single_25perS_02

description: 80kb resolution data

value: FALSE

tag: cell cycle phase


title: Control3

value: non targeting siRNA


title: CBMS1_Day2Diff_ESC_single_25perS_03

description: 80kb resolution data


title: CBMS1_ESC_single_75perS_59

description: 80kb resolution data

source_name: CBMS1 ESC

value: embryonic stem cell


title: CBMS1_Day2Diff_ESC_single_25perS_01

description: 80kb resolution data


title: OCH-202  chronic hepatitis C

value: chronic hepatitis C

tag: age


title: OCH-203  chronic hepatitis C

value: HCV


title: Control2


title: OCH-201  chronic hepatitis C


title: CBMS1_ESC_single_75perS_57

description: 80kb resolution data


title: OCH-204  chronic hepatitis C


title: Control1


title: CBMS1_ESC_single_75perS_56

description: 80kb resolution data


title: CBMS1_ESC_single_75perS_58

description: 80kb resolution data


title: CBMS1_ESC_single_75perS_55

description: 80kb resolution data


title: OCH-200  chronic hepatitis C


title: B_HeLa_shTop1_S2_L002_R1_HWGLVBCXY_V2

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

country: France

institute: IGH

data_processing:
Library strategy: i-BLESS (PMID: 30393778)
Base calls were performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2. Reads were aligned to the hg19 genome assembly using Bowtie 2 (version 2.1.0). Bigwig files were generated with the tool "Bamcompare" from Deeptool2.
Genome build: hg19
Supplementary files format and content: Bigwig files correspond to signal 10 bp step without any further smoothing.

source_name: i-BLESS of HeLa shTOP1 cells

growth_protocol: Cells were cultured in DMEM containing 10 % FCS and Penicillin/Streptomycin

extract_protocol: Ten million HeLa cells were resuspended in PBS buffer and mixed with 1% low melting point agarose in PBS buffer at 40°C. Cell suspension was mixed with liquid paraffin at 40 °C and vigorously shaken by hand for one minute, until emulsion was formed. The emulsion was then poured into ice-cold PBS buffer and the mixture was stirred for several minutes. Agarose bead suspension was gently centrifuged (200g, 10 min), paraffin layer was removed and agarose bead pellet was washed 3 times with TE buffer. Beads were washed with ES buffer (1% Sarkosyl, 25 mM EDTA, pH 8.0), resuspended in ES with 50 µg/mL Proteinase K and incubated overnight at 50 °C. After incubation, the beads were washed with TE + 0.1 mM PMSF and twice with TE. Next, the beads were washed in 1× Blunting Buffer (NEB), followed by DNA ends blunting using Quick Blunting kit (NEB) for 2 h and then washed twice with TE. The beads were subsequently washed with dA-Tailing Reaction Buffer (NEB) and DNA ends were A-tailed using NEBNext® dA-Tailing Module for 80 min. Next, the beads were washed with T4 ligation buffer and then resuspended in T4 ligation buffer with 100 nM P5 adapter and T4 ligase (NEB) and incubated overnight at 16 °C. After ligation, the beads were washed once with TE, and encapsulated DNA was initially sonicated using Covaris S220. Total DNA was isolated using Zymoclean™ Large Fragment DNA Recovery Kit (Zymo Research) and once again fragmented by sonication to create ~400 bp fragments. Labeled fragments were captured by streptavidin beads (Invitrogen), blunted and A-tailed using NEBNext® Ultra™ End Repair/dA-Tailing, then ligated to a P7 adapter. The resulting circular DNA was then linearized by USER (NEB) digestion and amplified and indexed by PCR using Illumina PCR primers. Quality and quantity of the resulting libraries were assessed on 2100 Bioanalyzer using HS DNA Kit (Agilent), and on Qubit 2.0 Fluorometer using Qubit dsDNA HS Assay Kit (Life Technologies). The libraries were sequenced (1x61 bp) on Illumina HiSeq2500 platform, according to the modified experimental and software protocols for generation of high-quality data for low-diversity samples, as previously described (PMID: 30393778).

treatment_protocol: Cells were treated with 2 microgram/ml of Doxycycline for 72 hr before the ChIP experiments.

tag: cell line

value: HeLa

tag: genotype

tag: treatment

value: untreated


title: CBMS1_ESC_single_75perS_53

description: 80kb resolution data


title: OCH-199  chronic hepatitis C

tag: disease state

tag: Sex

value: F

tag: bmi


title: B_HeLa_S1_L001_R1_HWGLVBCXY_V1

source_name: i-BLESS of HeLa cells

value: WT


title: OCH-198  chronic hepatitis C

source_name: liver tissue

tag: viral infection


title: CBMS1_ESC_single_75perS_51

description: 80kb resolution data


title: CBMS1_ESC_single_75perS_50

description: 80kb resolution data


title: Lund human mesencephalic cells (LUHMES) Run 3

city: New York

first: Matthew

middle: A

last: Lalli

state: NY

address: 1 Gustave L. Levy Pl

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

data_processing:
10x CellRanger v2.1
Read mapping (STAR v2.5)
CellRanger provides filtered gene barcode matrices that were then imported into Seurat for further analysis
Genome_build: hg38
Supplementary_files_format_and_content: .mtx file contains gene id (in RunX_genes.tsv files) (Cell barcodes in RunX_barcodes.tsv).  Lookup tables.csv contain the detected sgRNAs for each CellBarcode

molecule: polyA RNA

source_name: Lund human mesencephalic cells (LUHMES)

growth_protocol: LUHMES cells were cultured  as done in Scholz et al., 2011. Proliferating LUHMES cells were maintained in Dulbecco’s Modified Eagle Media (DMEM)/F12 media supplemented with 1% N2 and 40 ng/mL bFGF and 1% penicillin-streptomycin.  Cells were grown in T25 flasks coated with poly-ornithine and fibronectin.

extract_protocol: 3' polyA RNA seq; 10X Genomics Chromium Prep (v2)

treatment_protocol: dCas9-KRAB polyclonal LUHMES cells were infected with serial dilutions of pooled sgRNA lentivirus. Virus-containing media was removed after 4-6 hours of transduction. Antibiotic selection with puromycin (1 µg/mL) was applied 24 hours after infection. Wells in which no more than 25% of cells survived, corresponding to multiplicity of infection < 0.3, were used for experiments. Cells were expanded for 4 days before plating for differentiation. For differentiation, bFGF was withdrawn from the media and tetracycline was added (1 µg /mL) to repress the v-Myc transgene.  After re-plating, cells were differentiated for 6 to 8 days in the presence of tetracycline to allow efficient repression and differentiation. Puromycin and blasticidin were maintained for the duration of all experiments to ensure gRNA and dCas9-KRAB expression in all cells.

value: Lund human mesencephalic cells (LUHMES)

tag: Stage

value: differentiated neurons, day 8

value: female


title: OCH-197  chronic hepatitis C


title: CBMS1_ESC_single_75perS_48

description: 80kb resolution data

tag: cell type


title: CBMS1_ESC_single_75perS_49

description: 80kb resolution data

tag: strain


title: OCH-196  chronic hepatitis C


title: CBMS1_ESC_single_75perS_47

description: 80kb resolution data

tag: sample state


title: CBMS1_ESC_single_75perS_45

description: 80kb resolution data

tag: xx or xo chromosomes in single cell samples


title: CBMS1_ESC_single_75perS_44

description: 80kb resolution data

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)


title: Lund human mesencephalic cells (LUHMES) Run 1


title: CBMS1_ESC_single_75perS_43

description: 80kb resolution data

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)


title: CBMS1_ESC_single_75perS_42

description: 80kb resolution data

tag: repliscore of 40–70%


title: Subclone_Q8_BSseq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
BS-Seq sequences were trimmed with Trim Galore (v0.5.0; Cutadapt v1.15) with the default options. Trimmed sequences were mapped to the human GRCh38 genome using Bismark (Krueger and Andrews, 2011) (v0.17.0); CpG methylation calls were extracted and analyzed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Bisulfite data was analyzed using the freely available sequence data analysis software SeqMonk v1.38.2 (Andrews S; Babraham Bioinformatics). Quality control was performed within SeqMonk to assess average coverage and depth over features of interest. Duplicate clones cultured in different growth-conditions were analyzed as replicate sets; multiple subclones derived from each condition were analyzed as grouped data.  Analysis was performed using built-in quantification pipelines, with the stringency of analysis matched to the level and depth of coverage of samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: human pluripotent stem cell, MShef4

extract_protocol:
Genomic DNA was isolated (DNeasy kit, Qiagen) from each parental cell line, all clones and subclones
Libraries were prepared as previously described (von Meyenn et al. 2016) by sonicating 500ng genomic DNA using a Covaris Sonicator into 300-400bp long fragments, followed by end-repair, A-tailing and methylated adapter (Illumina) ligation using NEB NGS library preparation reagents.  Subsequently, libraries were bisulphite-treated using the EZ DNA Methylation-Direct Kit (Zymo), followed by library amplification with indexed primers using KAPA HiFi Uracil+ HotStart DNA Polymerase (Roche). All amplified libraries were purified using AMPure XP beads (Agencourt), and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer.

value: PSC


title: CBMS1_ESC_single_75perS_46

description: 80kb resolution data

tag: cell cycle phase


title: CBMS1_ESC_single_75perS_41

description: 80kb resolution data


title: Subclone_Q12_BSseq


title: CBMS1_ESC_single_75perS_54

description: 80kb resolution data

value: TRUE


title: Subclone_Q10_BSseq


title: CBMS1_ESC_single_75perS_40

description: 80kb resolution data


title: CBMS1_ESC_single_25perS_54

description: 80kb resolution data


title: OCH-193  chronic hepatitis C

tag: age


title: OCH-194  chronic hepatitis C


title: Subclone_P8_BSseq


title: CBMS1_ESC_single_25perS_53

description: 80kb resolution data


title: Lund human mesencephalic cells (LUHMES) Run 2

tag: cell line


title: Subclone_P4_BSseq


title: CBMS1_ESC_single_25perS_52

description: 80kb resolution data


title: CBMS1_ESC_single_25perS_51

description: 80kb resolution data


title: CBMS1_ESC_single_25perS_50

description: 80kb resolution data


title: OCH-195  chronic hepatitis C


title: OCH-190  chronic hepatitis C

value: M


title: Subclone_P2_BSseq


title: CBMS1_ESC_single_25perS_49

description: 80kb resolution data

value: CBA/MsM


title: CBMS1_ESC_single_25perS_48

description: 80kb resolution data

value: Single cell


title: OCH-188  chronic hepatitis C


title: phGC-nc rep4

city: Wuhan

first: Wei

last: Luo

state: Hubei

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province

institute: Huazhong Agricutural University

data_processing:
Reads were filtered by removing adapters, low quality reads and unknown bases
Clean reads were mapped to Gallus_gallus-5.0 of ensembl using HISAT2 v2.1.0
Genes expression level are quantified by a software package: stringtie v1.3.4d
Differentially expressed genes were calculated by Deseq2 v1.26.0
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM and reads count values for each Sample ...

organism: Gallus gallus

source_name: ovary

growth_protocol: The primary granulosa cells were pre-cultured with Medium 199 (Gibco, USA) and 5% FBS (Gibco, USA) overnight (16h).

extract_protocol:
Primary poGC and phGC transfected FOXL2-siRNA or NC-siRNA were named as poGC-KD, poGC-CT, phGC-KD and phGC-CT respectively. RNA library was prepared using a total amount of 1μg RNA per sample.
The sequencing library was generated under the instruction manual with NEB Next UltraTM RNA Library Prep Kit for Illumina (NEB, USA). Obtained sixteen cDNA libraries were sequenced on an Illumina Hiseq X-ten platform and generated paired-end reads.

treatment_protocol: The primary granulosa cells transfected with FOXL2-specific siRNA (FOXL2-siRNA) or NC nonsense siRNA (NC-siRNA) using Lipofectamine 3000 (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions, respectively.

value: White Leghorns

tag: tissue

value: follicle

value: granulosa

tag: development stage

value: pre-hierarchical

value: control


title: OCH-192  chronic hepatitis C

tag: disease state

value: chronic hepatitis C

value: HCV


title: OCH-187  chronic hepatitis C

tag: Sex


title: phGC-nc rep3

tag: treatment


title: Subclone_O4_BSseq


title: phGC-nc rep1


title: phGC-kd rep4

value: FOXL2 kd


title: Subclone_O10_BSseq


title: OCH-191  chronic hepatitis C

tag: bmi

tag: viral infection


title: phGC-kd rep3

tag: cell type


title: Subclone_N8_BSseq


title: phGC-kd rep2

tag: strain


title: phGC-kd rep1


title: Subclone_N7_BSseq


title: poGC-nc rep4

value: pre-ovulation


title: poGC-nc rep3


title: OCH-184  chronic hepatitis C

value: F


title: Subclone_O7_BSseq


title: Subclone_N10_BSseq


title: phGC-nc rep2


title: poGC-nc rep2


title: OCH-189  chronic hepatitis C


title: OCH-183  chronic hepatitis C


title: poGC-nc rep1


title: poGC-kd rep4


title: Subclone_J8_BSseq


title: poGC-kd rep3


title: OCH-182  chronic hepatitis C


title: poGC-kd rep1


title: OCH-185  chronic hepatitis C


title: susceptible.inoculated.day7.rep2

city: Gainesville

first: Weiming

last: Hu

state: FL

address: 1881 Natural Area Dr.

department: Entomology and Nematology

institute: University of Florida

description:
susceptible inoculated day7 rep2
KI72

data_processing:
Raw sequences were checked for quality using FastQC
reads with a quality score above 30 were aligned directly to the pepper reference genome Capsicum annuum vision 1.55 utilizing the program STAR
Gene counts were summarized by HTSeq-count, Differentially Expressed Genes (DEG) were calculated using R package “DESeq2”
The number of DEG shared across time points and treatments was calculated in R, and Venn diagram plots were generated using Venny2.1
Genome_build: capsicum annuum vision 1.55
Supplementary_files_format_and_content: processed data were stored in tab file, including the normalized abundance measurements of all samples

organism: Capsicum annuum

source_name: root

growth_protocol: The plants were grown in 100% sand, and watered daily

extract_protocol:
The whole root of the plants were extracted use Qiagen's plant mini RNA extraction kit
whole RNA was prepared following standard Illumina Hiseq protocol

treatment_protocol: The treatment plants were inoculated with 300  Meloidogyne incognita juveniles

value: root

tag: group

value: susceptible

tag: agent

value: RKN M. incognita

tag: time point


title: poGC-kd rep2


title: Subclone_J6_BSseq

value: PSC


title: Subclone_J5_BSseq


title: susceptible.inoculated.day7.rep3

description:
susceptible inoculated day7 rep3
KI73


title: Subclone_J20_BSseq


title: OCH-179  chronic hepatitis C


title: OCH-181  chronic hepatitis C


title: OCH-180  chronic hepatitis C


title: OCH-178  chronic hepatitis C


title: susceptible.inoculated.day7.rep1

description:
susceptible inoculated day7 rep1
KI71


title: susceptible.inoculated.day4.rep3

description:
susceptible inoculated day4 rep3
KI43


title: Subclone_J15_BSseq


title: Subclone_J1_BSseq


title: susceptible.inoculated.day1.rep2

description:
susceptible inoculated day1 rep2
KI12


title: susceptible.inoculated.day1.rep1

description:
susceptible inoculated day1 rep
KI11


title: susceptible.inoculated.day4.rep2

description:
susceptible inoculated day4 rep2
KI42


title: susceptible.inoculated.day1.rep3

description:
susceptible inoculated day1 rep3
KI13


title: susceptible.control.day7.rep3

description:
susceptible control day7 rep3
KC73


title: Subclone_J13_BSseq


title: susceptible.control.day7.rep2

description:
susceptible control day7 rep2
KC72


title: OCH-176  chronic hepatitis C


title: susceptible.inoculated.day4.rep1

description:
susceptible inoculated day4 rep1
KI41


title: MShef4_J8_BSseq


title: MShef4_J9_BSseq


title: MShef4_J7_BSseq


title: susceptible.control.day4.rep1

description:
susceptible control day4 rep1
KC41


title: susceptible.control.day4.rep3

description:
susceptible control day4 rep3
KC43


title: susceptible.control.day7.rep1

description:
susceptible control day7 rep1
KC71


title: susceptible.control.day1.rep2

description:
susceptible control day1 rep2
KC12


title: OCH-177  chronic hepatitis C

value: M


title: OCH-174  chronic hepatitis C


title: susceptible.control.day1.rep3

description:
susceptible control day1 rep3
KC13


title: OCH-173  chronic hepatitis C


title: susceptible.control.day4.rep2

description:
susceptible control day4 rep2
KC42


title: resistant.inoculated.day7.rep3

description:
resistant inoculated day7 rep3
CI73

value: resistant


title: OCH-175  chronic hepatitis C


title: OCH-171  chronic hepatitis C


title: MShef4_J5_BSseq


title: MShef4_J6_BSseq


title: MShef4_J4_BSseq


title: resistant.inoculated.day7.rep2

description:
resistant inoculated day7 rep2
CI72


title: OCH-170  chronic hepatitis C


title: OCH-169  chronic hepatitis C


title: resistant.inoculated.day7.rep1

description:
resistant inoculated day7 rep1
CI71


title: GmEM_Input_for_GLYMA.04G093300_br2

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads from technical replicates were combined and peaks were identified for each biological replicates using MACS2, using default parameters and a q value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2.

source_name: embryos

growth_protocol: Soybean cv Williams 82 plants were grown in 2 gallon pots containing Ron’s mix (1 part coarse sand, 1 part compost, 1 part peat moss, 3 pounds/yard Dolomite) in UC Davis greenhouses at temperatures ranging 22-30°C and under 16 hour-days.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 2 ug of an antibody raised against the peptide SRSQPQPQPLHPQYHH and ASGGVFSREE,  corresponding to the amino acids 117-132 and 170-180 of GLYMA.04G093300, respectively.  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow System V2, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Early maturation stage embryos were dissected from 6 to 7 mm seeds.  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

tag: cultivar

value: Williams 82

value: embryos

tag: Stage

value: early maturation stage

tag: antibody


title: GmEM_GLYMA.04G093300-ChIP-Ab2_br2

value: anti-peptide2 GLYMA.04G093300


title: GmEM_Input_for_GLYMA.04G093300_br1


title: MShef4_J2_BSseq


title: OCH-168  chronic hepatitis C

tag: age


title: MShef4_J20_BSseq


title: GmEM_GLYMA.04G093300-ChIP-Ab2_br1


title: susceptible.control.day1.rep1

description:
susceptible control day1 rep1
KC11


title: resistant.inoculated.day4.rep2

description:
resistant inoculated day4 rep2
CI42


title: GmEM_GLYMA.04G093300-ChIP-Ab1_br2

value: anti-peptide1 GLYMA.04G093300


title: resistant.inoculated.day4.rep1

description:
resistant inoculated day4 rep1
CI41


title: MShef4_J1_BSseq


title: resistant.inoculated.day1.rep3

description:
resistant inoculated day1 rep3
CI13


title: MShef4_J19_BSseq


title: GmEM_GLYMA.04G093300-ChIP-Ab1_br1


title: MShef4_J18_BSseq


title: MShef4_J3_BSseq


title: resistant.inoculated.day1.rep2

description:
resistant inoculated day1 rep2
CI12


title: GmEM_Input_for_GLYMA.07G038400_br2

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Peaks were identified for each biological replicates using MACS2, using default parameters and a q value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 2 ug of an antibody raised against the peptide STSSRPPDADFPPQD,  corresponding to the amino acids 188-202 of GLYMA.07G038400.  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow System V2, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit


title: OCH-166  chronic hepatitis C


title: OCH-165  chronic hepatitis C


title: OCH-164  chronic hepatitis C


title: GmEM_Input_for_GLYMA.07G038400_br1


title: resistant.inoculated.day4.rep3

description:
resistant inoculated day4 rep3
CI43


title: OCH-163  chronic hepatitis C


title: resistant.control.day7.rep2

description:
resistant control day7 rep2
CC72


title: resistant.control.day7.rep3

description:
resistant control day7 rep3
CC73


title: MShef4_J16_BSseq


title: MShef4_J15_BSseq


title: OCH-162  chronic hepatitis C


title: OCH-167  chronic hepatitis C


title: GmEM_GLYMA.07G038400-ChIP_br2

value: anti-peptide GLYMA.07G038400


title: resistant.control.day7.rep1

description:
resistant control day7 rep1
CC71


title: GmEM_GLYMA.07G038400-ChIP_br1


title: OCH-161  chronic hepatitis C

value: chronic hepatitis C


title: OCH-186  chronic hepatitis C

value: HCV


title: MShef4_J14_BSseq


title: OCH-172  chronic hepatitis C


title: resistant.control.day4.rep2

description:
resistant control day4 rep2
CC42


title: OCH-160  chronic hepatitis C


title: MShef4_J13_BSseq


title: MShef4_J12_BSseq


title: OCH-159  chronic hepatitis C


title: resistant.control.day4.rep1

description:
resistant control day4 rep1
CC41


title: MShef4_J17_BSseq


title: resistant.control.day1.rep3

description:
resistant control day1 rep3
CC13


title: MShef4_J11_BSseq


title: MShef4_J10_BSseq


title: OCH-158  chronic hepatitis C


title: Brd1+/- vehicle 8 [amygdala]

city: Aarhus c

first: Per

last: Qvist

state: Denmark

address: Hoegh Guldbergs Gade 10, Building 1116-460

department: Biomedicine

country: Denmark

institute: Aarhus University

data_processing:
A minimum of 10 million clean 50bp single-end reads were generated per sample, and all raw information was converted into a standard format with FastQ Groomer.
Quality control was performed on all samples using FastQC.
With a sliding window at 4, Trimmomatic scanned reads from  the 5’-end 4 bases at a time and cut the read if the average quality within the window  fell below the threshold of 20. If a read became shorter than 40 bp in length, it  was excluded from the analysis.
Reads that passed quality control (more than 90% bases having less than 1% sequencing error; No ambiguous bases) were mapped to the mouse genome (GRCm38.dna.toplevel.fa; Mus_musculus.GRCm38.90.gtf) using the HISAT2 alignment tool (version 2.1.0).
Aligned reads were counted, assembled into transcripts and quantified using StringTie (version 1.3.4).
Differentially Expressed Genes (DEGs) were identified by edgeR3.24.1 and reported after Benjamini-Hochberg false discovery rate (FDR) (5%) correction or as nominally significant DEGs (p<0.01).
Genome_build: Mus_musculus.GRCm38.90
Supplementary_files_format_and_content: CSV. TPM matrix

source_name: amygdala (AMG)

extract_protocol:
Brains were collected, snap frozen, sectioned and punched. RNA was extracted from brain punches using Maxwell-16 instrument system and LEV simplyRNA Tissue Kit.
RNA libraries were prepared for sequencing usingTruSeq library preparation kit and  protocol.

treatment_protocol: Saline injection (vehicle) or antidepressant drug (IMN or FLX)

value: amygdala (AMG)

value: vehicle

tag: genotype

value: female


title: OCH-157  chronic hepatitis C

value: F


title: OCH-156  chronic hepatitis C


title: resistant.control.day1.rep1

description:
resistant control day1 rep1
CC11

tag: tissue

value: root


title: Brd1+/- vehicle 7 [amygdala]


title: resistant.control.day1.rep2

description:
resistant control day1 rep2
CC12


title: MShef4_bulk_BSseq


title: resistant.control.day4.rep3

description:
resistant control day4 rep3
CC43


title: Liver GHR  Knockout

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description: Gene expression data from livrs at 8 weeks of age.

hyb_protocol: Affymetrix GeneChip® Mouse Gene 1.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

label: biotin

source_name: Liver GHR  Knockout

label_protocol: 100ng of total RNA were amplified and labeled using the Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

growth_protocol: Mice were kept under standard  animal husbandry

extract_protocol: RNAeasy Kit (Quiagen#74104)

treatment_protocol: Livers from the mice were dissected at 8 weeks of age and snap-frozen

tag: gender

value: male

value: liver

value: GHR knockout

value: 8 weeks


title: WT vehicle 8 [amygdala]

value: wildtype


title: Liver WT control

source_name: Liver WT control


title: Liver MDR2 Knockout

source_name: Liver MDR2 Knockout

value: MDR2 knockout


title: Liver GHR/MDR2 Double knockouts

source_name: Liver GHR/MDR2 Double knockouts

value: GHR/MDR2 Double knockouts


title: MShef11_Y27632_L9_BSseq

source_name: human pluripotent stem cell, MShef11

value: PSC

tag: culture condition


title: Brd1+/- IMN 9 [anterior cingulate cortex (aCC)]

data_processing:
A minimum of 10 million clean 50bp single-end reads were generated per sample, and all raw information was converted into a standard format with FastQ Groomer.
Quality control was performed on all samples using FastQC.
With a sliding window at 4, Trimmomatic scanned reads from  the 5’-end 4 bases at a time and cut the read if the average quality within the window  fell below the threshold of 20. If a read became shorter than 40 bp in length, it  was excluded from the analysis.
Reads that passed quality control (more than 90% bases having less than 1% sequenCing_error; No ambiguous bases) were mapped to the mouse genome (GRCm38.dna.toplevel.fa; Mus_musculus.GRCm38.90.gtf) using the HISAT2 alignment tool (version 2.1.0).
Aligned reads were counted, assembled into transcripts and quantified using StringTie (version 1.3.4).
Differentially Expressed Genes (DEGs) were identified by edgeR3.24.1 and reported after Benjamini-Hochberg false discovery rate (FDR) (5%) correction or as nominally significant DEGs (p<0.01).
Genome_build: GRCm38
Supplementary_files_format_and_content: TPM

source_name: anterior cingulate cortex (aCC)

extract_protocol:
Brains were collected, snap frozen, sectioned and punched. RNA was extracted from brain punches using Maxwell-16 instrument system and LEV simplyRNA Tissue Kit.
RNA libraries were prepared for sequenCing_using Beijing Genomics Institute (BGI) library preparation kits and protocols.

treatment_protocol: Saline injection (vehicle) or antidepressant drug (IMN)

value: anterior cingulate cortex (aCC)

value: imipramine 10 mg/kg

tag: Sex


title: Brd1+/- IMN 8 [anterior cingulate cortex (aCC)]

tag: treatment


title: OCH-155  chronic hepatitis C

tag: disease state

value: chronic hepatitis C

value: M

tag: bmi


title: OCH-154  chronic hepatitis C

tag: viral infection

value: HCV


title: MShef11_Y27632_L8_BSseq

tag: cell type


title: OCH-153  chronic hepatitis C


title: WT vehicle 7 [amygdala]

value: amygdala (AMG)

value: vehicle

tag: strain


title: WT vehicle 6 [amygdala]

value: female


title: WT IMN 10 [anterior cingulate cortex (aCC)]


title: OCH-151  chronic hepatitis C

value: F


title: WT IMN 9 [anterior cingulate cortex (aCC)]


title: MShef11_Y27632_L6_BSseq


title: WT vehicle 5 [amygdala]


title: MShef11_Y27632_L5_BSseq


title: Brd1+/- vehicle 9 [anterior cingulate cortex (aCC)]


title: OCH-150  chronic hepatitis C


title: Brd1+/- vehicle 5 [amygdala]


title: MShef11_Y27632_L4_BSseq


title: Brd1+/- vehicle 8 [anterior cingulate cortex (aCC)]


title: Brd1+/- vehicle 4 [amygdala]


title: OCH-149  chronic hepatitis C


title: MShef11_Y27632_L2_BSseq


title: MShef11_Y27632_L3_BSseq


title: OCH-148  chronic hepatitis C


title: WT vehicle 7 [anterior cingulate cortex (aCC)]


title: OCH-152  chronic hepatitis C


title: Brd1+/- IMN 7 [anterior cingulate cortex (aCC)]


title: CBMS1_ESC_single_75perS_52

description: 80kb resolution data

value: CBA/MsM

value: embryonic stem cell

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

value: FALSE

tag: cell cycle phase


title: MShef11_Y27632_L7_BSseq


title: Brd1+/- vehicle 6 [amygdala]

tag: genotype


title: WT vehicle 4 [amygdala]

tag: tissue

value: wildtype


title: Brd1+/- IMN 6 [anterior cingulate cortex (aCC)]


title: Brd1+/- vehicle 3 [amygdala]


title: MShef11_Y27632_L1_BSseq


title: WT vehicle 3 [amygdala]


title: WT vehicle 8 [anterior cingulate cortex (aCC)]


title: MShef11_Y27632_L10_BSseq


title: MShef11_Y27632_K9_BSseq


title: OCH-145  chronic hepatitis C

tag: age


title: Brd1+/- vehicle 1 [amygdala]


title: OCH-146  chronic hepatitis C


title: Brd1+/- IMN 5 [anterior cingulate cortex (aCC)]


title: MShef11_Y27632_K8_BSseq

tag: culture condition


title: WT IMN 8 [anterior cingulate cortex (aCC)]

tag: Sex


title: OCH-143  chronic hepatitis C


title: WT vehicle 2 [amygdala]

tag: treatment


title: MShef11_Y27632_K7_BSseq


title: Brd1+/- vehicle 2 [amygdala]


title: MShef11_Y27632_K6_BSseq


title: Brd1+/- IMN 8 [amygdala]


title: OCH-144  chronic hepatitis C

tag: disease state


title: OCH-141  chronic hepatitis C

tag: bmi


title: OCH-142  chronic hepatitis C

tag: viral infection


title: OCH-147  chronic hepatitis C


title: WT IMN 6 [anterior cingulate cortex (aCC)]


title: WT IMN 8 [amygdala]


title: WT IMN 5 [anterior cingulate cortex (aCC)]


title: MShef11_Y27632_K5_BSseq

tag: cell type


title: WT vehicle 1 [amygdala]

tag: strain


title: Brd1+/- vehicle 7 [anterior cingulate cortex (aCC)]


title: OCH-140  chronic hepatitis C


title: MShef11_Y27632_K4_BSseq


title: Brd1+/- vehicle 6 [anterior cingulate cortex (aCC)]


title: MShef11_Y27632_K3_BSseq


title: OCH-138  chronic hepatitis C


title: Brd1+/- vehicle 5 [anterior cingulate cortex (aCC)]


title: OCH-139  chronic hepatitis C


title: WT IMN 7 [anterior cingulate cortex (aCC)]


title: MShef11_Y27632_K1_BSseq


title: WT vehicle 6 [anterior cingulate cortex (aCC)]


title: OCH-136  chronic hepatitis C


title: OCH-137  chronic hepatitis C


title: Brd1+/- IMN 6 [amygdala]


title: WT vehicle 4 [anterior cingulate cortex (aCC)]


title: Brd1+/- IMN 5 [amygdala]


title: OCH-135  chronic hepatitis C


title: MShef11_standard_P8_BSseq

value: standard


title: OCH-134  chronic hepatitis C


title: MShef11_standard_P9_BSseq


title: Brd1+/- IMN 4 [anterior cingulate cortex (aCC)]


title: OCH-133  chronic hepatitis C


title: Brd1+/- IMN 7 [amygdala]


title: MShef11_Y27632_K2_BSseq


title: WT FLX 8 [amygdala]

value: fluoxetine 5 mg/kg


title: WT IMN 6 [amygdala]


title: Brd1+/- IMN 4 [amygdala]


title: MShef11_standard_P6_BSseq

value: PSC


title: OCH-132  chronic hepatitis C


title: WT IMN 7 [amygdala]


title: WT IMN 5 [amygdala]


title: MShef11_standard_P5_BSseq


title: MShef11_standard_P4_BSseq


title: OCH-131  chronic hepatitis C


title: WT IMN 4 [anterior cingulate cortex (aCC)]

value: anterior cingulate cortex (aCC)


title: MShef11_Y27632_K10_BSseq


title: Brd1+/- IMN 2 [anterior cingulate cortex (aCC)]

value: imipramine 10 mg/kg


title: OCH-130  chronic hepatitis C

value: chronic hepatitis C


title: WT vehicle 5 [anterior cingulate cortex (aCC)]


title: Brd1+/- FLX 8 [amygdala]


title: MShef11_standard_P3_BSseq


title: WT IMN 3 [anterior cingulate cortex (aCC)]


title: Brd1+/- FLX 7 [amygdala]


title: WT FLX 7 [amygdala]


title: Brd1+/- IMN 3 [anterior cingulate cortex (aCC)]


title: MShef11_standard_P1_BSseq


title: MShef11_standard_P2_BSseq


title: Brd1+/- FLX 6 [amygdala]


title: WT IMN 2 [anterior cingulate cortex (aCC)]


title: OCH-129  chronic hepatitis C


title: WT IMN 1 [anterior cingulate cortex (aCC)]


title: Brd1+/- FLX 5 [amygdala]


title: Brd1+/- IMN 3 [amygdala]


title: MShef11_standard_P10_BSseq


title: MShef11_standard_O9_BSseq


title: Brd1+/- vehicle 4 [anterior cingulate cortex (aCC)]


title: OCH-128  chronic hepatitis C

value: M


title: OCH-127  chronic hepatitis C

value: HCV


title: Brd1+/- vehicle 3 [anterior cingulate cortex (aCC)]


title: MShef11_standard_O8_BSseq


title: Brd1+/- vehicle 2 [anterior cingulate cortex (aCC)]


title: OCH-126  chronic hepatitis C


title: OCH-125  chronic hepatitis C


title: OCH-124  chronic hepatitis C


title: OCH-123  chronic hepatitis C


title: MShef11_standard_O7_BSseq


title: Brd1+/- vehicle 1 [anterior cingulate cortex (aCC)]


title: Brd1+/- FLX 4 [amygdala]

value: amygdala (AMG)


title: Brd1+/- IMN 2 [amygdala]


title: WT vehicle 3 [anterior cingulate cortex (aCC)]

value: vehicle


title: MShef11_standard_O6_BSseq


title: OCH-122  chronic hepatitis C


title: Brd1+/- FLX 3 [amygdala]

value: female


title: WT vehicle 2 [anterior cingulate cortex (aCC)]


title: Brd1+/- FLX 2 [amygdala]


title: MShef11_standard_O5_BSseq


title: MShef11_standard_O4_BSseq


title: WT vehicle 1 [anterior cingulate cortex (aCC)]


title: OCH-121  chronic hepatitis C


title: Brd1+/- IMN 1 [anterior cingulate cortex (aCC)]


title: Brd1+/- FLX 1 [amygdala]


title: OCH-120  chronic hepatitis C

value: F


title: Brd1+/- IMN 1 [amygdala]


title: WT FLX 6 [amygdala]


title: OCH-119  chronic hepatitis C


title: MShef11_standard_O2_BSseq


title: WT IMN 4 [amygdala]


title: Brd1+/- IMN 8

data_processing:
A minimum of 10 million clean 50bp single-end reads were generated per sample, and all raw information was converted into a standard format with FastQ Groomer.
Quality control was performed on all samples using FastQC.
With a sliding window at 4, Trimmomatic scanned reads from  the 5’-end 4 bases at a time and cut the read if the average quality within the window  fell below the threshold of 20. If a read became shorter than 40 bp in length, it  was excluded from the analysis.
Reads that passed quality control (more than 90% bases having less than 1% sequencing error; No ambiguous bases) were mapped to the mouse genome (GRCm38.dna.toplevel.fa; Mus_musculus.GRCm38.90.gtf) using the HISAT2 alignment tool (version 2.1.0).
Aligned reads were counted, assembled into transcripts and quantified using StringTie (version 1.3.4).
Differentially Expressed Genes (DEGs) were identified by edgeR3.24.1 and reported after Benjamini-Hochberg false discovery rate (FDR) (5%) correction or as nominally significant DEGs (p<0.01).
Supplementary_files_format_and_content: TPM

source_name: Striatum (CPu)

extract_protocol:
Brains were collected, snap frozen, sectioned and punched. RNA was extracted from brain punches using Maxwell-16 instrument system and LEV simplyRNA Tissue Kit.
RNA libraries were prepared for sequencing using Beijing Genomics Institute (BGI) library preparation kits and protocols.

value: Caudate Putamen (CPu)

value: imipramine 10mg/kg


title: WT IMN 8


title: WT FLX 5 [amygdala]


title: MShef11_standard_O1_BSseq


title: OCH-118  chronic hepatitis C


title: MShef11_standard_O10_BSseq


title: WT IMN 7


title: WT IMN 3 [amygdala]


title: MShef11_low_oxygen_Q9_BSseq

value: low oxygen


title: Brd1+/- vehicle 7


title: WT FLX 4 [amygdala]


title: MShef11_low_oxygen_Q8_BSseq


title: OCH-115  chronic hepatitis C


title: MShef11_standard_O3_BSseq


title: WT vehicle 8


title: WT FLX 3 [amygdala]


title: OCH-114  chronic hepatitis C


title: WT IMN 2 [amygdala]


title: WT vehicle 7


title: OCH-113  chronic hepatitis C


title: MShef11_low_oxygen_Q6_BSseq


title: MShef11_low_oxygen_Q7_BSseq


title: OCH-112  chronic hepatitis C


title: OCH-117  chronic hepatitis C


title: MShef11_low_oxygen_Q5_BSseq


title: Brd1+/- IMN 7


title: OCH-111  chronic hepatitis C


title: OCH-116  chronic hepatitis C


title: MShef11_low_oxygen_Q4_BSseq


title: Brd1+/- IMN 5


title: WT FLX 1 [amygdala]


title: MShef11_low_oxygen_Q3_BSseq


title: WT IMN 1 [amygdala]


title: OCH-110  chronic hepatitis C


title: OCH-109  chronic hepatitis C


title: WT IMN 6


title: WT IMN 5


title: MShef11_low_oxygen_Q2_BSseq


title: OCH-108  chronic hepatitis C


title: WT IMN 4


title: shRai1_BIC_rep3

city: Ann Arbor

first: Patricia

last: Garay

state: MI

address: 1137 Catherine St 5815 Med Sci II

institute: University of Michigan

description: nascent RNA

data_processing:
Full length reads were mapped to mm9 using TopHat2 (v2.1.0) with Bowtie2 (v2.2.6), using BBDUK (v35.51) to trim adaptors 2-30 bp (k=30, mink=2, minlength=15, hdist=1). Only uniquely mapping reads were analyzed further.
BAM Files were converted to Bigwig files in a strand specific manner. Bigwigs were normalized to 10 million non-rRNA and non-mitochondrial reads.
DESeq2 was used to call differential gene expression between TTX-treated, BIC-treated, and vehicle-treated samples, and between shCtrl and shRai1 treated samples (model built incorporating biological replicate effect; beta prior=true; alpha=0.05).
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files represent genome coverage by the reads in a strand specific manner after normalizing to 10 million non-rRNA non-mtRNA reads. DESeq2 files represent differential gene expression between pairs of samples (incorporating biological replicates).

source_name: mouse forebrain cultures

growth_protocol: Mouse forebrain tissue was dissected from E18 embryos, cells were dissociated and plated on poly-D-lysine coated coverslips in Neurobasal medium with 2.5% FBS, 1X B27 supplement, 25 uM beta-mercaptoethanol, and 0.5 mM Glutamax. Half-volume feeds of medium without FBS were performed every 3-4 days.

extract_protocol:
Cells were homogenized in TRI Reagent BD (Sigma) and RNA isolated by phenol-bromocholoropropane extraction.
RNA was fragmented and adapters were ligated directly to 3' end of RNAs. Nascent RNA was isolated using bromouridine-antibody-conjugated beads (Santa Cruz), and library preparation was derived from an adaptation of the Illumina Tru-seq protocol.

treatment_protocol: On day in vitro (DIV) 14, cells were infected with lentivirus containing control or Rai1-targeted shRNA. On DIV 17, neurons were treated for 4 hours with tetrodotoxin-citrate (TTX, Tocris, 1 uM final concentration) or bicuculline-methiodide (BIC, Abcam, 20 uM final concentration) or vehicle (water). After 3 hours and 40 minutes of treatment, bromouridine (Sigma, 2 mM final concentration) was added for 20 minutes before cell harvest.

tag: shRNA

value: BIC

tag: day in vitro harvested

tag: embryonic day


title: shRai1_BIC_rep2

description: nascent RNA


title: shRai1_BIC_rep1

description: nascent RNA


title: WT FLX 2 [amygdala]

value: wildtype


title: Brd1+/- vehicle 6


title: Brd1+/- IMN 6


title: MShef11_low_oxygen_Q12_BSseq


title: MShef11_low_oxygen_Q11_BSseq


title: shRai1_TTX_rep3

description: nascent RNA

value: TTX


title: Brd1+/- vehicle 5


title: Brd1+/- vehicle 4


title: MShef11_low_oxygen_Q10_BSseq


title: OCH-106  chronic hepatitis C


title: shRai1_TTX_rep2

description: nascent RNA


title: OCH-105  chronic hepatitis C


title: WT vehicle 6


title: MShef11_low_oxygen_N8_BSseq


title: shRai1_TTX_rep1

description: nascent RNA


title: MShef11_low_oxygen_N7_BSseq


title: OCH-104  chronic hepatitis C


title: WT vehicle 5


title: MShef11_low_oxygen_Q1_BSseq


title: shRai1_Veh_rep3

description: nascent RNA


title: OCH-102  chronic hepatitis C


title: OCH-103  chronic hepatitis C


title: shRai1_Veh_rep2

description: nascent RNA


title: MShef11_low_oxygen_N6_BSseq


title: OCH-107  chronic hepatitis C


title: Brd1+/- IMN 4


title: shRai1_Veh_rep1

description: nascent RNA


title: MShef11_low_oxygen_N5_BSseq


title: shCtrl_BIC_rep3

description: nascent RNA

value: shCtrl


title: OCH-101  chronic hepatitis C


title: Brd1+/- IMN 3


title: Brd1+/- IMN 2


title: WT IMN 3


title: MShef11_low_oxygen_N2_BSseq

value: PSC


title: MShef11_low_oxygen_N4_BSseq


title: shCtrl_TTX_rep3

description: nascent RNA


title: shCtrl_BIC_rep2

description: nascent RNA


title: Brd1+/- IMN 1


title: MShef11_low_oxygen_N3_BSseq


title: MShef11_low_oxygen_N1_BSseq


title: shCtrl_TTX_rep2

description: nascent RNA


title: WT IMN 2


title: MShef11_bulk


title: microglia_with PGC-1α_rep 2

city: Tianjin

first: Bin

last: Han

address: 154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

description: Gene expression in microglia with PGC-1α overexpression

hyb_protocol: Labeled controls and test samples labeled with Cy5-dCTP were dissolved in 80 μL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: After washing, slides were scanned immediately using G2565CA (Agilent Technologies).

data_processing: The array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13 (Agilent). To select the differentially expressed genes, we used thresholdvalues of ≥2 and ≤−2-fold change and Benjamini-Hochberg corrected p vlaue of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage. Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).

source_name: microglia_with PGC-1α

label_protocol: cDNA labeled with a fluorescent dye (Cy5-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. The procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

extract_protocol: Total RNA was extracted from microglia by using  the Trizol reagent (Invitrogen) and purified with a NucleoSpin® RNA clean-up kit (MACHEREY- NAGEL, Germany) according to manufacter’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Only RNA extracts with RNA integrity number values >6 underwent in further analysis.

value: Microglia

tag: gender

value: male

value: PGC-1{alpha} overexpression


title: Clone_G8_BSseq


title: E4Ki_E4Mixed (scRNA-seq)

city: San Francisco

first: Kelly

last: Zalocusky

address: 1650 Owens Street, Gladstone Center for Translational Advancement

institute: Gladstone Institutes

description: hIPSC-derived apoE4 neurons transplanted into the E4KI mouse hippocamps, allowed to mature for 7 months. Collected with surrounding hippocampal tissue.

data_processing:
aligned with STAR using Cellranger v.2.0.1
UMIs assigned to barcodes and counted using Cellranger v.2.0.1
filtered UMI count matrices was loaded into Seurat v.2.3.4
Data were filtered to include only protein coding genes. Cells were filtered to include only cells with 100–1000 genes detected, 100–2000 UMI, and <0.05% mitochondrial reads
gene expression matrices were then log-normalized with a scale of factor of 10,000
Genome_build: GRCh38-3.3.0
Supplementary_files_format_and_content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

organism:
Homo sapiens
Mus musculus

source_name: neurons / brain cells

growth_protocol: Mixed hiPSC-derived neuronal populations were derived based on methods developed previously from our lab (Wang et al., 2018). Three 10cm-dishes (Corning) of 85% confluent hiPSCs-were dissociated with a brief treatment of Accutase (Millipore). After hiPSCs were dissociated, Accutase was neutralized by addition of equal volume of N2B27 medium (50% DMEM/F12 (Gibco), 50% Neurobasal Medium (Gibco), 1% NEAA (Gibco), 1% Glutamax (Gibco), 0.5% Pen/Strep (Gibco), 1X N2 Supplement [ Stock 100X] (Gibco), 1X B27 Supplement [Stock 50X] (Gibco)). hiPSCs were centrifuged and re-suspended in N2B27 medium with the addition of 10 mM SB (Stemgent) and 0.25 mM LDN (Stemgent) as well as 10 mM Rock Inhibitor (Tocris) in a T-175 flask (Thermo Scientific). After 24 hours, hiPSCs formed small spheres (neurospheres) and were centrifuged and resuspended in SB and LDN only. This was repeated every 48-hours until 7 days post differentiation. On day 7, the neurospheres were plated down onto two 10cm dishes coated with growth factor reduced Matrigel (Corning) and allowed to form neuronal rosettes. During this time rosettes were sustained by N2B27 media alone and half of the media was replaced every 48-72 hours depending on confluency. On day 20, rosettes had formed immature neuronal populations and were dissociated for maturation. Rosettes were treated with Accutase for 10-15 minutes until they dissociated under gentle pipetting. Once dissociated, neuronal progenitors were filtered through a 40 mm strainer (Fischer) to ensure a single cell suspension. They were then plated into tissue culture plates that were first coated with Poly-L-Lysine  (Sigma, 0.1 mg/mL) overnight at 37°C, washed 3X with DPBS (Gibco) and then coated with Laminin (Gibco, 6 mg/mL) overnight at 37°C. Neurons were plated in N2B27 medium supplemented with 10 mM DAPT (Tocris), 10 ng/mL BDNF (Peprotech), and 10 ng/mL GDNF (Peprotech) for one week, after which DAPT was removed and BDNF and GDNF were maintained.

extract_protocol:
Hippocampi were isolated from single hemispheres of mice at the time of euthanasia, immediately frozen in dry ice and stored at -80°C. For isolation of human nuclei, hippocampi were thawed and incubated in HEB (BrainBits LLC)(1mL/ hippocampi) and kept on ice. 2mL chilled lysis buffer was then added to the tissue and was homogenized with 21G needle. Tissue was lysed on ice for 15 minutes and swirled to mix. This was repeated 3 times during incubation. Lysed hippocampi were titrated 5-7 times with 1mL pipette. Lysate was then washed in 30mm MACS Smart Strainer to remove large clumps and then centrifuged at 500g for 5 minutes are 4°C. Supernatant was aspirated and pellet was washed with 1mL Nuclei Wash and Resuspension Buffer. Nuclei were centrifuged at 500g for 5 min at 4°C and supernatant was then aspirated. The nuclear pellet was resuspended in 500mL staining buffer (0.5% RNase-free BSA and 0.2 mg/mL RNasin Plus RNAse inhibitory in RNAse-free PBS) and incubated for 15 minutes on ice to allow for blocking of non-specific antibody binding. 100mL of samples were removed for negative control staining. After blocking, anti-human nuclear antigen antibody conjugated to phycoerythrin was added to the nuclei solution [1:100] and incubated at 4°C for 30 minutes rotating. After incubation, samples were washed by adding 500mL of staining buffer to each tube and inverting several times. Samples were then collected by centrifugation for 5 min at 400g at 4°C. Supernatant was aspirated, and nuclei were resuspended in 500mL staining buffer for FACS sorting, with DAPI (0.1 mg/mL) added directly before sorting on Aria FACS sorter (BD Biosciences).
cDNA libraries were prepared using the Chromium Single Cell 3′ Library and Gel Bead kit v3 (10x Genomics: 1000092) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 sequencer at the UCSF CAT Core.

treatment_protocol: Neurons (D28–35; i.e., +1-+2 weeks maturation) were washed in 1X PBS which was then aspirated and replaced with warm Accutase (Millipore) for 15 minutes or until neurons dissociated with gentle tapping. Accutase was neutralized with N2B27 medium to bring total volume >30 mL and then cells were filtered through a 40 mm strainer (Fisher) to ensure a single cell suspension. Single cells were then centrifuged and resuspended to concentration of 1000 cells/nL in 1X HBSS (Gibco) supplemented with 10 ng/mL BDNF (Peprotech),10 ng/mL GDNF (Peprotech) and 100 ng/mL DNAseI (Roche) and kept at 4°C for transplantation. ApoE4-KI and apoE3-KI mice were anesthetized with an intraperitoneal injection of ketamine (60 mg/kg) and xylazine (30 mg/kg) and maintained on 0.8–1.0% isofluorane (Henry Schein). The head was secured with earbars and a tooth bar in a stereotaxic alignment system (Kopf Instruments). Fur was removed from the scalp, which was then sterilized with alternating swabs of chlorhexidine and 70% ethanol. The scalp was opened and sterilized with 3% hydrogen peroxide. Cell suspensions (~1000 cells/nL) were loaded into ~60 mm tip diameter, 30° beveled glass micropipette needles (Nanoject, Drummon Scientific Company). Bilateral rostral and caudal stereotaxic sites were drilled with a 0.5 mm microburr (Foredom, Fine Science Tools), and the coordinates used for hilar transplantation were X = ±1.65, Y = 2.00, Z = 1.7 and X = ± 2.90,Y = 3.20, Z = 2.2, with Z measured from the surface of the brain (David Kopf Instruments). At each transplantation site, ~20nL (~20,000 cells) were injected and allowed to diffuse for 3 min. For recovery, mice were sutured with 6–0 monofilament nonabsorbent nylon sutures (Ethicon), administered analgesics ketophen (5 mg/kg subcutaneously) and buprenorphine (0.0375 mg/kg intraperitoneally), and monitored on a heating pad until ambulatory.

value: transplanted hIPSC-derived neurons and surrounding hippocampal brain cells

value: Transplanted into E4KI Mouse Brain

value: human cells:ApoE4; mouse cells:E4KI


title: MShef11_low_oxygen_N10_BSseq


title: Brd1+/- vehicle 3

value: vehicle


title: shCtrl_Veh_rep2

description: nascent RNA


title: microglia_with PGC-1α_rep 3


title: Clone_G2_BSseq


title: shCtrl_Veh_rep1

description: nascent RNA


title: microglia_without PGC-1α_rep 2

description: Gene expression in microglia without PGC-1α overexpression

source_name: microglia_without PGC-1α

value: without PGC-1{alpha} overexpression


title: microglia_with PGC-1α_rep 1


title: microglia_without PGC-1α_rep 3


title: shCtrl_TTX_rep1

description: nascent RNA


title: Clone_F1_BSseq


title: microglia_without PGC-1α_rep 1


title: Brd1+/- vehicle 1

value: female


title: WT vehicle 4

value: Caudate Putamen (CPu)


title: WT vehicle 3


title: WT IMN 1

value: imipramine 10mg/kg


title: Brd1+/- vehicle 2


title: Clone_E7_BSseq


title: E4Ki_E3Mixed (scRNA-seq)

description: hIPSC-derived isogenic apoE3 neurons transplanted into the E4KI mouse hippocamps, allowed to mature for 7 months. Collected with surrounding hippocampal tissue.

value: human cells:isogenic ApoE3; mouse cells:E4KI


title: Clone_F4_BSseq


title: E3Ki_E3Mixed (scRNA-seq)

description: hIPSC-derived isogenic apoE3 neurons transplanted into the E3KI mouse hippocamps, allowed to mature for 7 months. Collected with surrounding hippocampal tissue.

value: Transplanted into E3KI Mouse Brain

value: human cells:isogenic ApoE3; mouse cells:E3KI


title: E3Ki_E4Mixed (scRNA-seq)

description: hIPSC-derived apoE4 neurons transplanted into the E3KI mouse hippocamps, allowed to mature for 7 months. Collected with surrounding hippocampal tissue.

value: human cells:ApoE4; mouse cells:E3KI


title: Clone_E4_BSseq


title: Clone_B8_BSseq


title: WT vehicle 1

value: wildtype


title: Technical replicate 8

status: Public on Jun 19 2020

type: genomic

city: Diepenbeek

first: Michelle

last: Plusquin

address: Campus Diepenbeek Agoralaan Gebouw D

country: Belgium

institute: Hasselt University

description: Technical replicate 8

hyb_protocol: Bisulphite converted DNA (using the Zymo EZ DNA methylationTM kit - Zymo, Irvine, CA, USA) was hybridized to Illumina HumanMethylation 450K BeadChip arrays

scan_protocol: Arrays were scanned using an Illumina iScan

data_processing:
An in-house software written for the R statistical computing environment was used to preprocess the data as follows: removal of probes based on signal intensities and control probes, background subtraction and dye bias correction (for probes using the Infinium II design). Additionally, data were trimmed removing the outliers as defined by observations exceeding three interquartile ranges below the first quartile or above the fourth quartile. Sample failing quality control and with potential sex mismatch were removed.
normalized Average Beta in supplementary file

label: Cy3, Cy5

source_name: cholangiocyte cell line MMNK-1

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from buffy coats according to standard protocol

value: cholangiocyte cell line MMNK-1


title: Technical replicate 7

description: Technical replicate 7


title: Technical replicate 6

description: Technical replicate 6


title: Technical replicate 5

description: Technical replicate 5


title: WT vehicle 2


title: Cord blood ID_57

description: excluded: no data denoising covariates

source_name: cord blood

value: cord blood

tag: birthweight


title: Cord blood ID_91

description: excluded: no data denoising covariates


title: Cord blood ID_215

description: excluded: no data denoising covariates


title: Technical replicate 1

description: Technical replicate 1


title: Technical replicate 3

description: Technical replicate 3


title: Cord blood ID_503

description: excluded: failed preprocessing


title: Cord blood ID_112

description: excluded: no data denoising covariates


title: Cord blood ID_158

description: excluded: no data denoising covariates


title: Cord blood ID_205

description: excluded: no data denoising covariates


title: Technical replicate 2

description: Technical replicate 2


title: Cord blood ID_327

description: excluded: no data denoising covariates


title: Cord blood ID_204

description: excluded: no data denoising covariates


title: Cord blood ID_367

description: excluded: no data denoising covariates


title: Cord blood ID_323

description: excluded: failed preprocessing


title: Cord blood ID_307

description: excluded: failed preprocessing


title: Cord blood ID_108

description: excluded: failed preprocessing


title: Cord blood ID_401

description: excluded: failed preprocessing


title: Technical replicate 4

description: Technical replicate 4


title: Cord blood ID_278

description: excluded: failed preprocessing


title: Cord blood ID_397

description: excluded: no data denoising covariates


title: Cord blood ID_391

description: excluded: failed preprocessing


title: Cord blood ID_439

description: excluded: no data denoising covariates


title: Cord blood ID_417

description: excluded: no data denoising covariates


title: Cord blood ID_490

description: excluded: failed preprocessing


title: Cord blood ID_328

description: excluded: failed preprocessing


title: Cord blood ID_134

description: excluded: failed preprocessing


title: Cord blood ID_121

description: excluded: failed preprocessing


title: Cord blood ID_99


title: Cord blood ID_379

description: excluded: failed preprocessing


title: Cord blood ID_96


title: Cord blood ID_97


title: Cord blood ID_98


title: Cord blood ID_89


title: Cord blood ID_86


title: Cord blood ID_95


title: Cord blood ID_88


title: Cord blood ID_87


title: Cord blood ID_93


title: Cord blood ID_84


title: Cord blood ID_90


title: Cord blood ID_9


title: Cord blood ID_85


title: Cord blood ID_83


title: Cord blood ID_8


title: Cord blood ID_92


title: Cord blood ID_94


title: Cord blood ID_80


title: Cord blood ID_82


title: Cord blood ID_81


title: Cord blood ID_78


title: Cord blood ID_79


title: Cord blood ID_77


title: Cord blood ID_76


title: Fibroid [MP313F]

city: Houston

first: Katayoun

last: Rezvani

state: Texas

address: 1515 Holcombe Blvd

department: Department of Stem Cell Transplantation and Cellular Therapy

institute: The University of Texas MD Anderson Cancer Center

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: Raw IDAT files were processed using R package SeSAMe with noob background correction, non-linear dye bias correction, and non-detection masking. Methylation beta values were called as quantitative percentage of methylated signals over both unmethylated and methylated signals ranging from 0 to 1, with “0” indicating full lack of methylation and “1” full methylation. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies and implemented in SeSAMe.

label: Cy5 and Cy3

source_name: Fibroid

extract_protocol: DNA was quantified by Qubit fluorimetry (Life Technologies) and 500ng of DNA from each sample was bisulfite converted using the Zymo EZ DNA Methylation Kit (Zymo Research, Irvine, CA USA) following the manufacturer’s protocol using the specified modifications for the Illumina Infinium Methylation Assay.  After conversion, all bisulfite reactions were cleaned using the Zymo-Spin binding columns, and eluted in 12 uL of Tris buffer. Following elution, BS converted DNA was processed through the EPIC array protocol. To perform the assay, 7uL of converted DNA was denatured with 1ul 0.4N sodium hydroxide.  DNA was then amplified, hybridized to the EPIC bead chip, and an extension reaction was performed using flurophore labeled nucleotides per the manufacturer’s protocol.  Array beadchips were scanned on the Illumina iScan platform.  DNA methylome was captured by HumanMethylationEPIC (EPIC) BeadChip (Illumina, CA, USA) using the manufacturer’s standard protocol.

tag: subject id

tag: tissue type

value: Fibroid


title: Cord blood ID_75

tag: tissue


title: Cord blood ID_74


title: Cord blood ID_73


title: Cord blood ID_66


title: Cord blood ID_7


title: Cord blood ID_68


title: Cord blood ID_72


title: Cord blood ID_65


title: Cord blood ID_6


title: Cord blood ID_60


title: Cord blood ID_62


title: Fibroid [MP314F]

description: DNA was quantified by Qubit fluorimetry (Life Technologies) and 500ng of DNA from each sample was bisulfite converted using the Zymo EZ DNA Methylation Kit (Zymo Research, Irvine, CA USA) following the manufacturer’s protocol using the specified modifications for the Illumina Infinium Methylation Assay.  After conversion, all bisulfite reactions were cleaned using the Zymo-Spin binding columns, and eluted in 12 uL of Tris buffer. Following elution, BS converted DNA was processed through the EPIC array protocol. To perform the assay, 7uL of converted DNA was denatured with 1ul 0.4N sodium hydroxide.  DNA was then amplified, hybridized to the EPIC bead chip, and an extension reaction was performed using flurophore labeled nucleotides per the manufacturer’s protocol.


title: Normal Myometrium [MP313N]

source_name: Normal Myometrium

value: Normal Myometrium


title: Stromal Cervix [MP314C]

source_name: Stromal Cervix

value: Stromal Cervix


title: Cord blood ID_67


title: Cord blood ID_63


title: Cord blood ID_69


title: Cord blood ID_64


title: Cord blood ID_56


title: Cord blood ID_71


title: Cord blood ID_61


title: Normal Myometrium [MP314N]


title: Cord blood ID_59


title: Cord blood ID_58


title: Cord blood ID_54


title: Stromal Cervix [MP313C]


title: Cord blood ID_53


title: Cord blood ID_52


title: Cord blood ID_55


title: Cord blood ID_50


title: Cord blood ID_5


title: Cord blood ID_51


title: Cord blood ID_496


title: Cord blood ID_497


title: Cord blood ID_498


title: Cord blood ID_489


title: Cord blood ID_491


title: Cord blood ID_494


title: Cord blood ID_482


title: Cord blood ID_495


title: Cord blood ID_488


title: Cord blood ID_493


title: Cord blood ID_492


title: Cord blood ID_480


title: Cord blood ID_481


title: Cord blood ID_499


title: Cord blood ID_478


title: Cord blood ID_49


title: Cord blood ID_487


title: Cord blood ID_475


title: Cord blood ID_483


title: Cord blood ID_485


title: Cord blood ID_484


title: Cord blood ID_479


title: Cord blood ID_474


title: Cord blood ID_48


title: Cord blood ID_473


title: Cord blood ID_477


title: Cord blood ID_476


title: Cord blood ID_486


title: Cord blood ID_470


title: Cord blood ID_466


title: Cord blood ID_469


title: Cord blood ID_464


title: Cord blood ID_465


title: Cord blood ID_458


title: Cord blood ID_459


title: Cord blood ID_461


title: Cord blood ID_467


title: Cord blood ID_463


title: Cord blood ID_462


title: Cord blood ID_456


title: Cord blood ID_472


title: Cord blood ID_460


title: Cord blood ID_46


title: Cord blood ID_457


title: Cord blood ID_455


title: Cord blood ID_454


title: Cord blood ID_453


title: Cord blood ID_471


title: Cord blood ID_45


title: Cord blood ID_47


title: Cord blood ID_448


title: Cord blood ID_452


title: Cord blood ID_450


title: Cord blood ID_449


title: Cord blood ID_446


title: Cord blood ID_445


title: Cord blood ID_447


title: Cord blood ID_444


title: Cord blood ID_436


title: Cord blood ID_437


title: Cord blood ID_44


title: Cord blood ID_440


title: Cord blood ID_435


title: Cord blood ID_433


title: Cord blood ID_434


title: Cord blood ID_432


title: Cord blood ID_451


title: Cord blood ID_43


title: Cord blood ID_431


title: Cord blood ID_430


title: Cord blood ID_428


title: Cord blood ID_429


title: Cord blood ID_427


title: Cord blood ID_422


title: Cord blood ID_425


title: Cord blood ID_423


title: Cord blood ID_424


title: Cord blood ID_421


title: Cord blood ID_420


title: Cord blood ID_42


title: Cord blood ID_441


title: Cord blood ID_438


title: Cord blood ID_418


title: Cord blood ID_419


title: Cord blood ID_414


title: Cord blood ID_415


title: Cord blood ID_416


title: Cord blood ID_413


title: Cord blood ID_41


title: Cord blood ID_40


title: Cord blood ID_405


title: Cord blood ID_412


title: Cord blood ID_410


title: Cord blood ID_403


title: Cord blood ID_4


title: Cord blood ID_408


title: Cord blood ID_411


title: Cord blood ID_394


title: Cord blood ID_70


title: Cord blood ID_404


title: Cord blood ID_402


title: Cord blood ID_406


title: Cord blood ID_399


title: Cord blood ID_396


title: Cord blood ID_395


title: Cord blood ID_388


title: Cord blood ID_392


title: Cord blood ID_386


title: Cord blood ID_382


title: JWEAU-C6 rep 1

city: Birmingham

first: Olaf

last: Kutsch

state: AL

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
Adapter trimmed using TrimGalore (Babraham Bioinformatics).
All samples passed metrics by FastQC.
Alligned to hg19 using STAR.
Gene read counts quantified using HTSeq.
Normalized counts calculated and differential expression analyzed using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated table containing raw counts. Rows are genes and columns are samples.

source_name: Jurkat

growth_protocol: Cells were cultured in RPMI 1640 with 10% FBS and Pen./Strep.

extract_protocol:
RNA was extracted using Trizol and cleaned up with Qiagen RNEasy Mini kit.
Poly-A selection, reverse transcription, and Illumina library preparation were performed by Genewiz (Plainfield, NJ) using standard protocols.

tag: hiv infection

value: Latently Infected

tag: cd3 response

value: Unresponsive


title: Cord blood ID_409


title: Jurkat rep 2

value: Uninfected

value: Responsive


title: Jurkat rep 1


title: Cord blood ID_390


title: Cord blood ID_38


title: Cord blood ID_407


title: Cord blood ID_400


title: JWEAU-C6 rep 2


title: PDP-8-RNA rep2

city: Beijing

first: Zonggui

last: Chen

state: Beijing

address: No.5 Yiheyuan Road Haidian District

department: Academy for Advanced Interdisciplinary Studies

institute: Peking University

data_processing:
Basecalls performed using Illumina version 1.9
Reads were removed adapter sequences using cutadapt version 1.18 and deduplicated using FastUniq
RNA-seq reads were aligned to the hg19 genome assembly using hisat2 version 2.1.0 with parameter --mp 4,2
Alignments with mismatch (not induced by SNPs) were extract by python scripts.
Any other results were analysed by python scripts.
Genome_build: hg19
Supplementary_files_format_and_content: csv file contains fragment count, FPM and half-life; mismatch count of fragment csv file contains "mismatch count" and "fragment count" columns; gene level mismatch count of fragment csv files contain the combine of mismatch count and fragment count at the last column.

growth_protocol: HEK293T cells were grown at 37 °C in DMEM containing 10% FBS and 1% P/S.

extract_protocol:
3×10^6 HEK293T cells were seeded per 10-cm cell dish and grown for 24 h. For T > C conversion identification, 0 or 50 μM s4U was added to the medium and grown for another 24 h; For mRNA half-life calculation, 500 μM s4U was added to the medium and grown for 1 h; For PDP-mediated RNA dynamic analysis, PDP (0 or 4 or 8 μM) was added to the medium for 20 min prior to 1 h 500 μM s4U incubation. After that, RNA samples for library construction were prepared by total RNA extraction, polyadenylated RNA isolation, gDNA removal, RNA fragmentation and  acrylonitrile treatment. For T > C conversion identification, we named the RNA samples as Con-RNA (no s4U treatment, no acrylonitrile treatment), s4U-RNA (s4U treatment, no acrylonitrile treatment), Con-acrylonitrile-RNA (no s4U treatment, acrylonitrile treatment) and s4U-acrylonitrile-RNA (s4U treatment, acrylonitrile treatment), respectively. For mRNA half-life calculation, we named the RNA samples as halflife-RNA.  For PDP-mediated RNA dynamic analysis,  we named the RNA samples as PDP-0-RNA (no PDP treatment), PDP-4-RNA (4 μM PDP treatment) and PDP-8-RNA (8 μM PDP treatment), respectively.
Standard RNA seq libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB) according to manufacturer’s instructions. Sequencing was performed on Illumina Illumina HiSeq X Ten.

tag: cell line

value: human embryonic kidney cell line

value: PDP 8 μM + 500 μM s4U


title: Cord blood ID_377


title: PDP-0-RNA rep2

tag: treatment

value: PDP 0 μM + 500 μM s4U


title: Cord blood ID_375


title: Cord blood ID_385


title: JWEAU-A10 rep 2


title: Cord blood ID_384


title: JWEAU-A10 rep 1


title: Cord blood ID_373


title: Cord blood ID_372


title: s4U-acrylonitrile-RNA rep1

value: 500 μM s4U + acrylonitrile


title: Cord blood ID_383


title: Cord blood ID_381


title: Con-acrylonitrile-RNA rep1

value: no s4U treatment, acrylonitrile treatment


title: Cord blood ID_380


title: PDP-8-RNA rep1


title: s4U-RNA rep1

value: 50 μM s4U


title: Cord blood ID_370


title: BV2 cells_with PGC-1α_rep 1

source_name: BV2 cells with PGC-1α overexpression

extract_protocol: Total RNA was extracted from BV2 cells by using  the Trizol reagent (Invitrogen) and purified with a NucleoSpin® RNA clean-up kit (MACHEREY- NAGEL, Germany) according to manufacter’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Only RNA extracts with RNA integrity number values >6 underwent in further analysis.

value: BV2 cells

tag: genotype/variation

value: PGC-1alpha overexpression

value: LPS


title: BV2 cells_without PGC-1α_rep 3

source_name: BV2 cells without PGC-1α overexpression


title: Cord blood ID_39

value: cord blood


title: PDP-4-RNA rep2

value: PDP 4 μM + 500 μM s4U


title: Cord blood ID_378


title: PDP-4-RNA rep1


title: BV2 cells_without PGC-1α_rep 2


title: Con-RNA rep1

value: no s4U treatment, no acrylonitrile treatment


title: BV2 cells_with PGC-1α_rep 2


title: Cord blood ID_365


title: Cord blood ID_366


title: Cord blood ID_368


title: Cord blood ID_374


title: s4U-acrylonitrile-RNA rep2


title: BV2 cells_with PGC-1α_rep 3


title: PDP-0-RNA rep1


title: Con-acrylonitrile-RNA rep2


title: BV2 cells_without PGC-1α_rep 1


title: s4U-RNA rep2


title: Con-RNA rep2


title: Cord blood ID_371


title: Cord blood ID_369


title: Cord blood ID_37


title: Cord blood ID_36


title: Cord blood ID_364