title: Encapsulated human myoblasts implanted in an old mouse - rep2


title: Uterine fibroids patients gut microbiota Replicate 29

status: Public on Mar 05 2022

type: genomic

city: Changsha City of Hunan Province

first: xuan

last: peng

state: Hunan

address: 88 Xiangya Road

country: China

institute: Kaifu District, Changsha City, Hunan Province

description: Biological replicate 29 of 42.uterine fibroids patients gut microbiota

hyb_protocol: Oligoarray control targets and hybridization buffer provided by the manufacturer were added, and 500ng labeled sample DNA were applied to microarrays enclosed in the hybrid cassette. After hybridization, slides were washed sequential.

scan_protocol: Scans were performed on a GenePix4000B scanner.Images were quantified using Bluefuse software.

data_processing:
LOWESS normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Bluefuse software was used.
The output.txt is the result from fluorescence array. All information about array was demonstrated in the head of output.txt file.
The output.xls.result.txt is the relative abundances of each identified species, which are calculated base on fluorescence value in output.txt.
The relative abundances of each identified species, which are calculated base on the program,which first calculated the mean intensities of the 3 replicated spots corresponding to each species for the Cy5 and Cy3 channels. The mean Cy5/Cy3 ratio was calculated from the mean intensity of the two channels. The species were ranked by their mean signal intensity from which the background fluorescent signal was calculated from the median of mean intensity of the lower 30% of the species. For a species to be judged as positive detection, its mean signal intensity must be 10 fold above the background fluorescent signal. To calculate the relative abundance of the positive species, we normalize the mean Cy5/Cy3 ratios of all the positive species and the percentage of each species  multiply a fix factor 100000, and round up the result ,which is presented as the relative abundance value.

molecule: genomic DNA

organism: human feces metagenome

source_name: Uterine fibroids patient fecal microbiota

label_protocol: 10-20ng of DNA was amplified by PCR reaction with 16S universal primers.5ul PCR product was labelled with Bst enzyme and random primers at 45°C for 3 hours.The labeled product was stained with 20 μg of Cy5 dye and dissolved at 100 ng/ul after precipitation.

extract_protocol: Total DNA extracted  following manufacturer's instructions

tag: age

tag: condition

value: Uterine fibroids

tag: cell type

value: fecal microbiota

organism: synthetic construct

source_name: Internal reference provided by the manufacturer

tag: sample type

value: Internal reference (synthetic oligos)

tag: concentration


title: T5C_ArcC5GFAP_F1

type: SRA

city: Irvine

first: Ali

last: Mortazavi

state: CA

address: 2300E Biological Sciences III

country: USA

institute: UC Irvine

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole cortex. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).

library_source: transcriptomic

data_processing:
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Paired-end RNA-seq reads were aligned to mm10 reference genome and annotated to Gencode v21 transcriptome using STAR v.5.1 (Dobin et al.  2013).
Gene expression was calculated using RSEM v1.2.25 (Li and Dewey  2011).
Possible noise introduced by batch effects was corrected by the R (version 3.6.2) package Combat-seq (Zhang et al.  2020).
Data was then normalized using edgeR trimmed mean of M-values (TMM) function (Robinson et al.  2010). TPM was calculated utilizing a custom script and ComBat-seq batch corrected counts as input
Genome_build: mm10
Supplementary_files_format_and_content: RSEM output tab-delimited text files with abundance measures in counts and TPM

molecule: polyA RNA

organism: Mus musculus

source_name: cortex

extract_protocol:
Total RNA of each tissue was extracted using the QIAGEN RNeasy mini kit and QIAcube (Qiagen # 80204 and # 9002864)
Smart-seq2 protocol (Picelli et al.  2013); Nextera DNA Flex Library Prep Kit (20018704  Illumina);

tag: Sex

value: Female

value: 5 months

tag: genotype

value: Arctic mouse model of ADtic mice overexpressing C5a under the GFAP promoter


title: P2336_N714-S522

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

data_processing:
Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Reads were demultiplexed according to the Nextera XT dual indexes.
Libraries were inspected with the FastQC suite to assess the quality of the reads.
Paired-end reads were aligned to the human reference genome and gene expression was quantified with the GEMTools 1.7.0 RNASeq pipeline.
Genome_build: Assembly GRCh38, Gencode release 27
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as UMI counts for each cell (columns).

organism: Homo sapiens

source_name: HeLa (ATCC CCL-2)

growth_protocol: All the cell lines used in this article has been authenticated by StemElite ID (Promega). HeLa (ATCC CCL-2), Huh7 and A549 cell lines were grown in Dulbecco's Modified Eagle Medium—DMEM, high glucose, GlutaMAX-I, with pyruvate (Gibco)—supplemented with 10% fetal bovine serum (FBS, Hyclone) and penicillin-streptomycin (Sigma) in a 37°C humidified incubator with ~5% CO2.

extract_protocol:
Prior to the sorting, HeLa cells were trypsinized and resuspended in PBS with 5 mM EDTA. Then, cells were sorted on a SY3200 cell sorter (Sony Biotechnology)into 96-well plate which contained 3 μL of lysis Buffer. The plate was previously prepared with the lysis buffer and stored at -70°C. After the sorting, the plate was immediately frozen in carbonic ice and sent for RNA sequencing.
Full-length single cell RNA sequencing libraries are prepared using the Smart-seq2 protocol (Picelli et al., Nat. Protoc. 2014) with minor modifications. Briefly, freshly harvested cells were sorted into 96-well plates containing the lysis buffer. Reverse transcription was performed using SuperScrpit II (Invitrogen) in the presence of oligo-dT30VN, template-switching oligonucleotides and betaine. The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kappa Biosystems), ISPCR primer and 23 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity are assessed on a Bioanalyzer using a High Sensitvity DNA Kit (Agilent Technologies). 150 pg of the amplified cDNA were fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers. Products were purified twice with Agencourt Ampure XP beads and quantified again using a Bioanalyzer High Sensitvity DNA Kit. Sequencing of Nextera libraries was carried out on a Illumina HiSeq2500 v4.

treatment_protocol: To assay the extreme metabolic conditions cells were grown for at least two weeks (chronic adaptation) in DMEM, no glucose, no glutamine, no phenol Red (Gibco), and supplemented with 4.5 g/l of D-(+)-Glucose (Sigma) or with 2 mM L-glutamine (Gibco). We used 10 mM of non-metabolizable D-(+)-Galactose (Sigma) to maintain the osmotic pressure when glucose was removed.

value: epitheloid cervix carcinoma cell line

tag: cell line

value: HeLa (ATCC CCL-2)


title: T5H_ArcC5GFAP_M1

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole hippocampus. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).

source_name: hippocampus

value: Male


title: T5C_ArcC5GFAP_M1


title: Uterine fibroids patients gut microbiota Replicate 35

description: Biological replicate 35 of 42.uterine fibroids patients gut microbiota


title: Encapsulated human myoblasts implanted in an old mouse - rep1

type: RNA

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol  Standard Illumina scanning protocol

data_processing:
Data have been extracted using GenomeStudio software V2011.1 (Illumina). GenomeStudio identified missing bead types. We decided not to impute missing data, resulting in the exclusion of missing bead types for all the microarrays of the experiment. Number of retained probes is 31942.
Log2 quantile normalised signal intensity, encapsulted myoblasts were quantile normalised separetely from the connective tissues and blanks. Only the normalised myoblasts were considered in the differential expression analysis.

label: biotin

molecule: total RNA

source_name: Encapsulated human skeletal myoblasts

label_protocol: Two rounds cRNA synthesis starting with 5 ng of total RNA using MessageAmp™ II aRNA amplification kit (AM1751) and MessageAmp™ II-biotin enhanced aRNA amplification kit (AM1791,  Life Technologies, Carlsbad, California, USA) following provider recommandations.

extract_protocol: RNA was extracted using RNAdvance Tissue Kit (Beckman Coulter). Quality control was performed with Fragment Analyzer (Advanced Analytical)

tag: tissue/cell type

value: myoblasts from a capsule implanted in an old mouse

tag: implantation recipient mouse strain

tag: implantation recipient mouse age

value: young; 1.5 months


title: P2336_N714-S520


title: Uterine fibroids patients gut microbiota Replicate 27

description: Biological replicate 27 of 42.uterine fibroids patients gut microbiota


title: P2336_N714-S521


title: Uterine fibroids patients gut microbiota Replicate 26

description: Biological replicate 26 of 42.uterine fibroids patients gut microbiota


title: P2336_N715-S518


title: Uterine fibroids patients gut microbiota Replicate 25

description: Biological replicate 25 of 42.uterine fibroids patients gut microbiota


title: T5H_C5GFAP_F1

value: WT mice overexpressing C5a under the GFAP promoter


title: Encapsulated human myoblasts implanted in a young mouse - rep5

value: myoblasts from a capsule implanted in a young mouse


title: Encapsulated human myoblasts implanted in a young mouse - rep4


title: P2336_N714-S518


title: Encapsulated human myoblasts implanted in a young mouse - rep3


title: Uterine fibroids patients gut microbiota Replicate 24

description: Biological replicate 24 of 42.uterine fibroids patients gut microbiota


title: P2336_N714-S517


title: P2336_N714-S516


title: Uterine fibroids patients gut microbiota Replicate 22

description: Biological replicate 22 of 42.uterine fibroids patients gut microbiota


title: T5H_C5GFAP_M1


title: Uterine fibroids patients gut microbiota Replicate 23

description: Biological replicate 23 of 42.uterine fibroids patients gut microbiota


title: T5C_C5GFAP_M1


title: Encapsulated human myoblasts implanted in a young mouse - rep2


title: P2336_N714-S515


title: Encapsulated human myoblasts implanted in a young mouse - rep1


title: Uterine fibroids patients gut microbiota Replicate 28

description: Biological replicate 28 of 42.uterine fibroids patients gut microbiota


title: Uterine fibroids patients gut microbiota Replicate 21

description: Biological replicate 21 of 42.uterine fibroids patients gut microbiota


title: P2336_N714-S513


title: T5H_ArcC5KO_F1

value: Arctic mouse model of ADtic mice with C5ar1 knocked out (constitutive KO)


title: BEAS_DieselPollen_24h_CA_rep3

city: Munich

first: Joana

last: Candeias

address: Biedersteinerstr. 29

department: Center Allergy and Environment (ZAUM)

country: Germany

institute: Technical University Munich & Helmholtz Center Munich

description: Gene expression after 24h in 4 mg whole birch pollen exposure, primed with clean air 24h earlier

hyb_protocol: The Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes with Agilent fragmentation mix, according to the manufacturers instructions. After that, 25uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and 40uL of the samples was hybridized to One-Color SurePrint G3 8x60K Human gene expression arrays (Agilent Technologies, Inc, Waldbronn, Germany) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After incubation time, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1, at 500rpm and 1 minute with 32°C GE Wash buffer 2 (Agilent), at 500rpm. Slide was placed in a array gasket chamber for scan procedure.

scan_protocol: Slides were scanned using the Agilent DNA Microarray Scanner using one color scan setting for 8x60k G3 array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: Scanned images were analyzed with Feature Extraction Software Version 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20200924) to obtain background and Processed Signal intensities.

source_name: BEAS-2B cells

label_protocol: RNA samples (input of 100ng) were spiked (One-Color RNA Spike-in Kit, Agilent Technologies, Waldbronn, Germany), Cy3-labelled (Low Input Quick Amp Labeling Kit, one-color, Agilent Technologies, Waldbronn, Germany) and purified on RNeasy mini spin columns (QIAGEN). Generated Cy3-labelled cRNA was quantified with NanoPhotometer® N60, IMPLEN, Munich, Germany.

extract_protocol: RNA was obtained with the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany), with additional 1% ß-Mercaptoethanol (Roth, Karlsruhe, Germany), according to the manufacturer’s protocol.  The quantification and quality of the RNA was assessed with an UV-vis spectrophotometer (NanoPhotometer® N60, IMPLEN, Munich, Germany) and the Agilent 2100 Bioanalyzer RNA Nano chip (Agilent Technologies, Waldbronn, Germany), respectively.

treatment_protocol: BEAS-2B cells were cultured in 6-well Transwells with BEGM Medium. After 24h, basal medium was changed, apical medium was removed and cells were kept in air-liquid interface for 24h, before exposure. For combined expousre, cells were exposed to diesel CAST model aerosol for 2hours (or clean air), in an vitro exposure system. After that, basal medium was changed and cells were placed in a cell culture incubator for 24 hours.  After that, all cells were exposed to 4 mg of whole birch pollen dispersing it with 0.5 bar pressured air into the Pollen Sedimentation Chamber, for different incubation times. Cells were kept all the time at 37°C and 5% CO2. For the pollen exposure alone, the same amount of birch pollen was used (4mg) and exposure was performed as explained above.

tag: time

value: air+pollen


title: T5C_ArcC5KO_F1


title: Uterine fibroids patients gut microbiota Replicate 20

description: Biological replicate 20 of 42.uterine fibroids patients gut microbiota


title: T5H_ArcC5KO_M1


title: T5C_ArcC5KO_M1


title: T5C_C5GFAP_F1


title: BEAS_DieselPollen_24h_CA_rep1


title: P2336_N712-S520


title: BEAS_DieselPollen_24h_CA_rep2


title: Uterine fibroids patients gut microbiota Replicate 18

description: Biological replicate 18 of 42.uterine fibroids patients gut microbiota


title: Uterine fibroids patients gut microbiota Replicate 17

description: Biological replicate 17 of 42.uterine fibroids patients gut microbiota


title: Uterine fibroids patients gut microbiota Replicate 19

description: Biological replicate 19 of 42.uterine fibroids patients gut microbiota


title: BEAS_DieselPollen_24h_Exp_rep2

description: Gene expression after 24h in 4 mg whole birch pollen exposure, primed with diesel CAST model aerosol 24h earlier

value: diesel+pollen


title: BEAS_DieselPollen_24h_Exp_rep3


title: P2336_N712-S518


title: BEAS_DieselPollen_6h_CA_rep3

description: Gene expression after 6h50min in 4 mg whole birch pollen exposure, primed with clean air 24h earlier


title: Uterine fibroids patients gut microbiota Replicate 16

description: Biological replicate 16 of 42.uterine fibroids patients gut microbiota


title: BEAS_DieselPollen_24h_Exp_rep1


title: T5C_C5KO_M1

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole cortex. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).

value: WT mice with C5ar1 knocked out (constitutive KO)


title: Uterine fibroids patients gut microbiota Replicate 15

description: Biological replicate 15 of 42.uterine fibroids patients gut microbiota

value: Uterine fibroids


title: T5H_C5KO_M1

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole hippocampus. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).


title: P2336_N712-S517


title: P2336_N712-S522


title: BEAS_DieselPollen_6h_CA_rep4


title: P2336_N712-S515


title: Uterine fibroids patients gut microbiota Replicate 14

description: Biological replicate 14 of 42.uterine fibroids patients gut microbiota

value: fecal microbiota


title: P2336_N712-S513


title: BEAS_DieselPollen_6h_CA_rep2


title: T5C_Arc_F1

value: Arc

value: Arctic mouse model of AD


title: T5H_Arc_F1

value: Female

value: 5 months


title: Uterine fibroids patients gut microbiota Replicate 13

description: Biological replicate 13 of 42.uterine fibroids patients gut microbiota

value: Internal reference (synthetic oligos)


title: T5H_C5KO_F1


title: P2336_N712-S521

value: epitheloid cervix carcinoma cell line

value: HeLa (ATCC CCL-2)


title: P2336_N711-S522


title: T5C_C5KO_F1


title: Uterine fibroids patients gut microbiota Replicate 12

description: Biological replicate 12 of 42.uterine fibroids patients gut microbiota


title: BEAS_DieselPollen_6h_Exp_rep4

description: Gene expression after 6h50min in 4 mg whole birch pollen exposure, primed with diesel CAST model aerosol 24h earlier


title: Uterine fibroids patients gut microbiota Replicate 11

description: Biological replicate 11 of 42.uterine fibroids patients gut microbiota


title: T5H_Arc_M1

value: Male


title: BEAS_DieselPollen_6h_CA_rep1


title: P2336_N712-S516


title: P2336_N711-S520


title: Uterine fibroids patients gut microbiota Replicate 10

description: Biological replicate 10 of 42.uterine fibroids patients gut microbiota


title: T5H_WT_F1

value: WT

value: Wild type


title: BEAS_DieselPollen_6h_Exp_rep3


title: T5C_Arc_M1


title: Uterine fibroids patients gut microbiota Replicate 9

description: Biological replicate 9 of 42.uterine fibroids patients gut microbiota


title: P2336_N711-S518


title: P2336_N711-S517


title: BEAS_DieselPollen_6h_Exp_rep1


title: BEAS_DieselPollen_2h_CA_rep4

description: Gene expression after 2h25min in 4 mg whole birch pollen exposure, primed with clean air 24h earlier


title: Uterine fibroids patients gut microbiota Replicate 8

description: Biological replicate 8 of 42.uterine fibroids patients gut microbiota


title: Uterine fibroids patients gut microbiota Replicate 7

description: Biological replicate 7 of 42.uterine fibroids patients gut microbiota


title: T5C_WT_F1


title: BEAS_DieselPollen_6h_Exp_rep2


title: P2336_N711-S516


title: Uterine fibroids patients gut microbiota Replicate 6

description: Biological replicate 6 of 42.uterine fibroids patients gut microbiota


title: T5C_WT_M1


title: T5H_WT_M1


title: P2336_N711-S515


title: P2336_N711-S513


title: Uterine fibroids patients gut microbiota Replicate 5

description: Biological replicate 5 of 42.uterine fibroids patients gut microbiota


title: Uterine fibroids patients gut microbiota Replicate 4

description: Biological replicate 4 of 42.uterine fibroids patients gut microbiota


title: BEAS_DieselPollen_2h_CA_rep1


title: BEAS_DieselPollen_2h_CA_rep3


title: P2336_N711-S521


title: T2C_ArcC5GFAP_F1

value: 2 months

value: Arctic mouse model of ADtic mice overexpressing C5a under the GFAP promoter


title: P2336_N710-S522


title: T2H_C5GFAP_F4

value: WT mice overexpressing C5a under the GFAP promoter


title: Uterine fibroids patients gut microbiota Replicate 3

description: Biological replicate 3 of 42.uterine fibroids patients gut microbiota


title: BEAS_DieselPollen_2h_Exp_rep4

description: Gene expression after 2h25min in 4 mg whole birch pollen exposure, primed with diesel CAST model aerosol 24h earlier

value: diesel+pollen


title: BEAS_DieselPollen_2h_Exp_rep3


title: Uterine fibroids patients gut microbiota Replicate 2

description: Biological replicate 2 of 42.uterine fibroids patients gut microbiota


title: BEAS_DieselPollen_2h_Exp_rep2


title: T2C_C5GFAP_F4

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole cortex. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).


title: P2336_N710-S520


title: P2336_N710-S518


title: Hilar lymph node Patient 16

city: München

first: Laura

last: Sellmer

address: Ziemssenstrasse 1

institute: Department of Medicine V

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK193-4

hyb_protocol: Labelling, hybridization and scanning was performed on the nCounter platform according to manufacturer's instructions (Nanostring Technologies nCounter Analysis System, Seattle, USA). Gene expression profiling was performed using the IO 360 panel.

data_processing: Raw gene expression data was analyzed via Nanostring's nSolver 4.0 software. Quality control steps as well as normalization of data was performed.

source_name: Tumor-free hilar lymph node

extract_protocol: 10 um-thick FFPE sections were prepared for the extraction of total RNA from tumor cell-rich areas, affected lymph nodes and medistinal and hilar lymph nodes. Areas of interest were identified by a expert pathologist using H&E staings and overlaying with cut FFPE sections. Extracion was performed using Qiagen FFPE RNEasy kits and mRNA concentration was measured via Nanodrop.

tag: tissue

value: Tumor-free hilar lymph node

tag: overall survival

tag: censored overall survival

value: Yes

tag: progression-free survival

tag: censored progression-free survival

value: No

tag: age at diagnosis in years

tag: stage at diagnosis


title: T2H_C5GFAP_M4

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole hippocampus. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).

tag: age


title: P2336_N710-S517

tag: cell type


title: T2C_C5GFAP_M4


title: BEAS_DieselPollen_2h_Exp_rep1

tag: condition


title: BEAS_DieselPollen_2h_CA_rep2

value: air+pollen


title: Uterine fibroids patients gut microbiota Replicate 1

description: Biological replicate 1 of 42.uterine fibroids patients gut microbiota

value: Uterine fibroids

value: fecal microbiota

tag: sample type

tag: concentration


title: T2H_ArcC5KO_F3

tag: Sex

value: Female

tag: genotype

value: Arctic mouse model of ADtic mice with C5ar1 knocked out (constitutive KO)


title: T2H_ArcC5GFAP_F1


title: Hilar lymph node Patient 15

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK182-4

scan_protocol: Labelling, hybridization and scanning was performed on the nCounter platform according to manufacturer's instructions (Nanostring Technologies nCounter Analysis System, Seattle, USA). Gene expression profiling was performed using the IO 360 panel.


title: BEAS_4mg_24h_Pollen_rep3

description: Gene expression after 24h in 4 mg whole birch pollen exposure

value: pollen


title: P2336_N710-S515

value: epitheloid cervix carcinoma cell line

tag: cell line

value: HeLa (ATCC CCL-2)


title: BEAS_4mg_24h_Pollen_rep2


title: T2C_ArcC5KO_F3


title: Hilar lymph node Patient 14

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK175-4

label_protocol: Labelling, hybridization and scanning was performed on the nCounter platform according to manufacturer's instructions (Nanostring Technologies nCounter Analysis System, Seattle, USA). Gene expression profiling was performed using the IO 360 panel.


title: BEAS_4mg_24h_Pollen_rep1


title: Hilar lymph node Patient 13

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK173-4

value: Male


title: P2336_N710-S513


title: P2336_N710-S521


title: BEAS_4mg_24h_Air_rep3

description: Gene expression control sample of 24h in 4 mg whole birch pollen exposure

value: air


title: Hilar lymph node Patient 12

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK164-4


title: T2C_ArcC5KO_M4

value: 2 months


title: T2H_C5KO_F3

value: WT mice with C5ar1 knocked out (constitutive KO)


title: BEAS_4mg_24h_Air_rep1


title: Hilar lymph node Patient 11

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK163-4


title: P2336_N707-S520


title: T2C_C5KO_F3


title: Hilar lymph node Patient 10

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK135-4


title: T2H_C5KO_M4


title: Hilar lymph node Patient 9

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK114-4


title: Hilar lymph node Patient 8

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK108-4


title: BEAS_4mg_6h50min_Pollen_rep3

description: Gene expression after 6h50min in 4 mg whole birch pollen exposure


title: BEAS_4mg_6h50min_Pollen_rep1


title: P2336_N707-S518


title: P2336_N710-S516


title: T2C_C5KO_M4


title: BEAS_4mg_6h50min_Pollen_rep2


title: P2336_N707-S516


title: T2H_ArcC5KO_M4


title: T2H_Arc_F1

value: Arc

value: Arctic mouse model of AD


title: Hilar lymph node Patient 7

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK083-4

value: Tumor-free hilar lymph node


title: P2336_N707-S517


title: BEAS_4mg_6h50min_Air_rep2

description: Gene expression control sample of 6h50min in 4 mg whole birch pollen exposure


title: BEAS_4mg_24h_Air_rep2


title: T2C_Arc_F1

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole cortex. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).


title: Hilar lymph node Patient 6

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK081-4

value: Yes


title: BEAS_4mg_6h50min_Air_rep1


title: Hilar lymph node Patient 5

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK080-4


title: T2H_Arc_M5

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole hippocampus. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).


title: P2336_N707-S513


title: P2336_N707-S521


title: P2336_N707-S522


title: Hilar lymph node Patient 4

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK047-4

value: No


title: T2C_Arc_M5


title: BEAS_4mg_2h25min_Pollen_rep2

description: Gene expression after 2h25min in 4 mg whole birch pollen exposure


title: Hilar lymph node Patient 3

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK034-4


title: P2336_N706-S522


title: P2336_N706-S521


title: Hilar lymph node Patient 2

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK025-4


title: T2C_WT_M5

value: WT

value: Wild type


title: T2H_WT_M4


title: BEAS_4mg_2h25min_Pollen_rep1


title: P2336_N706-S520


title: P2336_N706-S518


title: T2C_WT_M4


title: Hilar lymph node Patient 1

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK006-4


title: BEAS_4mg_2h25min_Air_rep3

description: Gene expression control sample of 2h25min in 4 mg whole birch pollen exposure


title: BEAS_4mg_6h50min_Air_rep3


title: T2H_ArcC5GFAP_M3

value: Arctic mouse model of ADtic mice overexpressing C5a under the GFAP promoter


title: P2336_N706-S517


title: T3_RNA-seq

city: East Lansing

first: Aritro

last: Sen

state: Michigan

address: 766 Service Rd., ISTB

department: Animal Science

institute: Michigan State University

data_processing:
After investigating the quality of the raw data (the quality was judged based on Illumina’s Q score, which represents the error rate at
each base, built on a log10 score), sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor
quality using Trimmomatic v.0.36. The trimmed reads were mapped to the reference mouse genome available on ENSEMBL (Mus musculus GRCm38) using the STAR aligner v.2.5.2b.
The STAR aligner uses a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: raw counts in txt files

source_name: Liver

extract_protocol:
Total RNA was extracted from freshly isolated liver tissues from the Placebo and DHT pellet liver samples using Qiagen RNeasy Plus Universal mini kit. The samples were sequenced using a 2x150bp Paired End (PE) configuration. The total number of reads/sample were 45-50 million. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq wereas converted into fastq files and de-multiplexed using Illumina'’s bcl2fastq 2.17 software. configuration. The total number of reads/sample were 45-50 million. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq wereas converted into fastq files and de-multiplexed using Illumina'’s bcl2fastq 2.17 software.
RNA sequencing libraries were prepared using 500 ng RNA, and the NEB Next Ultra RNA Library Prep Kit for Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA)

treatment_protocol: Liver tissues were isolated from Placebo control and DHT pellet treated PCOS mice

tag: strain background

value: Liver tissue

value: 15 weeks

tag: treatment

value: DHT pellet treated PCOS mice


title: BEAS_4mg_2h25min_Air_rep2

tag: time


title: P2336_N707-S515

value: epitheloid cervix carcinoma cell line


title: Mediastinal lymph node Patient 14

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK175-3

source_name: Tumor-free mediastinal lymph node

tag: tissue

value: Tumor-free mediastinal lymph node

tag: overall survival

value: Female


title: Mediastinal lymph node Patient 15

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK182-3

tag: censored overall survival

tag: progression-free survival


title: P2336_N706-S516

value: HeLa (ATCC CCL-2)


title: T2C_ArcC5GFAP_M3

value: Male

value: 2 months


title: T2_RNA-seq


title: BEAS_4mg_2h25min_Pollen_rep3

value: pollen


title: Mediastinal lymph node Patient 13

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK173-3

tag: censored progression-free survival

tag: age at diagnosis in years


title: P2336_N706-S515


title: BEAS_4mg_2h25min_Air_rep1

value: air


title: T2H_C5GFAP_F3

tag: age

value: WT mice overexpressing C5a under the GFAP promoter


title: P2336_N706-S513

tag: cell type


title: Mediastinal lymph node Patient 12

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK164-3

tag: stage at diagnosis


title: C3_RNA-seq

value: Placebo


title: T2H_WT_M5


title: T2C_C5GFAP_F3


title: P2336_N705-S522


title: Mediastinal lymph node Patient 11

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK163-3

value: No


title: P2336_N705-S521


title: C1_RNA-seq


title: T2C_C5GFAP_F2


title: P2336_N705-S520


title: Mediastinal lymph node Patient 10

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK135-3


title: cond_7OFF.F3

city: Cambridge

first: Luca

last: Pellegrinet

address: 80 Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

data_processing:
Reads were quaity-trimmed and adapters were removed using 'TrimGalore!' (option: - q 30). Reads were aligned to the mouse reference genome (UCSC mm10) using 'Tophat2' (options: --read-mismatch 1 --max-multihits 1 ) guided by ENSEMBL 92 gene models.
Genome_build: mm10
Supplementary_files_format_and_content: Reads counts per ENSEMBL 92 transcript obtained by 'featureCounts'.

source_name: liver

growth_protocol: The activity of the mice was not restricted, and they were maintained on a 12-h light/dark schedule. All mice were fed regular chow. All protocols were approved by the Home Office and the CRUK or Cambridge University ethical commitee.

extract_protocol:
Total RNA was extracted with Qiagen RNA isolation columns, and cDNA library was prepared from mRNA.
RNA seq poly A, SE50

treatment_protocol: Liver injury was achieved by i.p. administration of Carbon tetrachloride dissolved in 1/10 in oil at 0.5 µL/g body weight. MycER activation was achieved by daily i.p. administration of Tamoxifen (1mg).

value: 7 days after injury without MycER activation


title: T2H_C5GFAP_M3


title: C2_RNA-seq


title: Mediastinal lymph node Patient 8

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK108-3


title: cond_7OFF.F2


title: cond_7OFF.F1


title: Mediastinal lymph node Patient 16

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK193-3

value: Yes


title: P2336_N705-S516


title: T2H_ArcC5KO_F2

value: Arctic mouse model of ADtic mice with C5ar1 knocked out (constitutive KO)


title: T2C_C5GFAP_M3

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole cortex. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).


title: T1_RNA-seq

value: Liver tissue


title: cond_3OFF.E2

value: 3 days after injury without MycER activation


title: T2H_ArcC5KO_M3


title: Mediastinal lymph node Patient 7

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK083-3


title: T2C_ArcC5KO_F2


title: cond_3OFF.E3


title: P2336_N705-S513


title: Mediastinal lymph node Patient 4

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK047-3


title: P2336_N705-S517


title: Mediastinal lymph node Patient 6

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK081-3


title: cond_3OFF.E1


title: Mediastinal lymph node Patient 5

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK080-3


title: T2C_ArcC5KO_M3


title: cond_2OFF.D3

value: 2 days after injury without MycER activation


title: T2H_C5KO_F2

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole hippocampus. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).

value: WT mice with C5ar1 knocked out (constitutive KO)


title: Mediastinal lymph node Patient 2

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK025-3

value: Tumor-free mediastinal lymph node


title: P2336_N704-S522

value: epitheloid cervix carcinoma cell line


title: Mediastinal lymph node Patient 1

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK006-3


title: Mediastinal lymph node Patient 3

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK034-3


title: P2336_N704-S521

value: HeLa (ATCC CCL-2)


title: cond_2OFF.D2


title: T2H_C5GFAP_F2

value: Female


title: T2C_C5KO_M3

value: Male

value: 2 months


title: P2336_N705-S515


title: T2C_C5KO_F2


title: P2336_N705-S518


title: P2336_N704-S516


title: T2H_C5KO_M3


title: T2H_C5KO_M2


title: Mediastinal lymph node Patient 9

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK114-3


title: P2336_N704-S520


title: T2C_C5KO_M2


title: P2336_N704-S515


title: cond_1OFF.C3

value: 1 days after injury without MycER activation


title: Affected lymph node Patient 16

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK193-2

source_name: Affected lymph node

value: Affected lymph node


title: cond_1OFF.C1


title: cond_12ON.B3

value: 12 days after injury with MycER activation


title: P2336_N704-S517


title: P2336_N704-S518


title: T2H_Arc_M4

value: Arc

value: Arctic mouse model of AD


title: P2336_N704-S513


title: cond_12ON.B2


title: Affected lymph node Patient 15

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK182-2

value: No


title: Affected lymph node Patient 13

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK173-2


title: Affected lymph node Patient 14

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK175-2


title: cond_1OFF.C2


title: Affected lymph node Patient 12

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK164-2


title: T2C_Arc_M4


title: cond_2OFF.D1


title: P2336_N703-S522


title: T2H_WT_F2

value: WT

value: Wild type


title: Affected lymph node Patient 11

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK163-2


title: cond_12ON.B1


title: cond_12.A3

value: 12 days after injury without MycER activation


title: Affected lymph node Patient 10

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK135-2


title: P2336_N703-S520


title: T2H_WT_M3


title: T2C_WT_F2

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole cortex. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).


title: P2336_N703-S518


title: Affected lymph node Patient 9

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK114-2


title: P2336_N703-S521


title: cond_12.A2


title: T2H_ArcC5GFAP_M2

value: Arctic mouse model of ADtic mice overexpressing C5a under the GFAP promoter


title: T2C_WT_M3


title: cond_12.A1


title: P2336_N703-S517


title: Affected lymph node Patient 7

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK083-2

value: Yes


title: P2336_N703-S516


title: T2C_ArcC5GFAP_M2


title: Affected lymph node Patient 6

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK081-2


title: I_CK rep 3

city: Lanzhou

first: Chai

last: Shujie

address: No.1 Yingmen Village, Anning District, Lanzhou city

institute: Gansu Agricultural University

data_processing:
cDNA libraries were sequenced on an Illumina HiSeq 2000 with 150 bp paired-end reads using  illumina  standard manufacturer’s protocols
Basecalls performed using the standard Illumina Genome Analyzer software and bcl2fastq version 2.0.1
Reads were trimmed for adaptor sequences and terminal nucleotides with Phred score less than 20 using Cutadapt version 1.18.
De novo transcriptome was assembled using Trinity version 2.3.2
RSEM version 1.3.1 was used across all samples to estimate transcript abundance against the Trinity-assembled transcriptome
Genome_build: Unigene.fa.gz (de novo assembly)
Supplementary_files_format_and_content: Trinity-assembled de novo sequences (fasta format) used as a reference for transcript abundance estimation

organism: Lupinus micranthus

source_name: Lupinus micranthus Guss

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaves

tag: treatment group

value: seedlings without treatment from Iceland seeds


title: P2336_N703-S515

value: epitheloid cervix carcinoma cell line

value: HeLa (ATCC CCL-2)


title: T2H_C5GFAP_F1

value: Female

value: WT mice overexpressing C5a under the GFAP promoter


title: Affected lymph node Patient 5

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK080-2

value: Male


title: Affected lymph node Patient 4

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK047-2

value: Affected lymph node


title: I_CK rep 2


title: I_CK rep 1


title: P2336_N703-S513


title: I_72h rep 3

value: seedlings treated with PEG drought for 72 hours from Iceland seeds


title: T2C_C5GFAP_F1

value: 2 months


title: P2336_N702-S522


title: P2336_N702-S521


title: Affected lymph node Patient 3

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK034-2


title: I_72h rep 1


title: I_72h rep 2


title: T2C_C5GFAP_M2


title: T2H_C5GFAP_M2

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole hippocampus. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).


title: P2336_N702-S520


title: P2336_N702-S518


title: Affected lymph node Patient 2

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK025-2


title: Affected lymph node Patient 8

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK108-2


title: Affected lymph node Patient 1

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK006-2


title: T2H_ArcC5KO_M2

value: Arctic mouse model of ADtic mice with C5ar1 knocked out (constitutive KO)


title: A_CK rep 2

value: seedlings without treatment from America seeds


title: Tumor Patient 16

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK193-1

source_name: Primary NSCLC tumor

value: Primary NSCLC tumor

value: No


title: I_24h rep 2

value: seedlings treated with PEG drought for 24 hours from Iceland seeds


title: P2336_N702-S517


title: T2H_ArcC5KO_M1


title: I_24h rep 3


title: T2H_C5KO_M1

value: WT mice with C5ar1 knocked out (constitutive KO)


title: Tumor Patient 15

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK182-1


title: P2336_N702-S513


title: I_24h rep 1


title: A_CK rep 3


title: T2C_C5KO_M1


title: Tumor Patient 13

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK173-1


title: P2336_N702-S516


title: T2H_Arc_M3

value: Arc

value: Arctic mouse model of AD


title: Tumor Patient 14

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK175-1


title: A_CK rep 1

value: leaves


title: T2C_ArcC5KO_M1


title: P2336_N701-S522

value: epitheloid cervix carcinoma cell line


title: A_72h rep 3

value: seedlings treated with PEG drought for 72 hours from America seeds


title: P2336_N701-S521

value: HeLa (ATCC CCL-2)


title: A_72h rep 2


title: Tumor Patient 12

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK164-1

value: Female


title: P2336_N701-S520


title: A_72h rep 1


title: T2C_Arc_M2

value: Male


title: Tumor Patient 11

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK163-1


title: A_24h rep 2

value: seedlings treated with PEG drought for 24 hours from America seeds


title: Tumor Patient 8

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK108-1


title: Tumor Patient 10

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK135-1


title: P2336_N702-S515


title: T2C_Arc_M3

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole cortex. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).


title: T2H_Arc_M2


title: A_24h rep 1


title: P2336_N701-S518


title: A_24h rep 3


title: P2336_N701-S515


title: T2C_ArcC5KO_M2


title: P2336_N701-S517


title: T2H_WT_F1

value: WT

value: Wild type


title: T2H_WT_M2

value: 2 months


title: Tumor Patient 7

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK083-1

value: Yes


title: T2C_WT_F1


title: P2336_N701-S513


title: Tumor Patient 6

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK081-1

value: Primary NSCLC tumor


title: Tumor Patient 3

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK034-1

value: No


title: T2C_WT_M2


title: Tumor Patient 5

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK080-1


title: Tumor Patient 4

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK047-1


title: UPP Pathway Specific Mutants 3_S60

city: Bloomington

first: Clay

last: Fuqua

state: IN

address: 1001 E. Third Street

department: Biology

institute: Indiana University

description:
GSF1944.S60.PoolTn-Seq
Illumina sequenced using transposon specific primers

library_source: genomic

data_processing:
Reads were quality and adapter trimmed w/ Trimmomatic (v0.33; ILLUMINACLIP:adapters.fa:2:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:20)
For files GSF1864 and GSF1944, sequencing would begin in transposon and only reads starting with the expected AACCTGTTA sequence were kept
Reads were mapped to the Agrobacterium tumefaciens C58 genome using bowtie2 (v2-2.3.2) with default parameters other than allowing for 2 alignments with -k 2 option
After mapping, reads with multiple equally good hits were excluded as ambiguous
Insertion locations were aggreagated with gene info using custom PERL scripts
Genome_build: Agrobacterium tumefaciens C58 (consisting of these molecules by Genbank ID: AE007869.2, AE007870.2, AE007871.2, AE007872.2)
Supplementary_files_format_and_content: tab-delimited files with header; file contains number of insertions at a given position in the genome along with annotation information

organism: Agrobacterium fabrum str. C58

source_name: Pooled G-DNA from cells in colonies

growth_protocol: Colonies with low UPP phenotype (low Congo Red staining) were cultured and pooled)

extract_protocol:
Total DNA extraction (Promega gDNA extraction kit))
DNA was sheared to 200-700 bp fragments.  Terminal deoxynucleotidyl transferase (TdT) tailed. PCR was used to append bar-coded aptamers specific for transposon insertions followed by those required for Illumina sequencing. 1M SE reads per sample were generated on Illumina NextSeq500 sequencer using a 75 high cycle sequencing kit and a custom sequencing primer.

value: delta_uppW mutant alone


title: Tumor Patient 2

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK025-1


title: UPP Pathway Specific Mutants 2_S73

description:
GSF1864.S73.PoolTn-Seq
Illumina sequenced using transposon specific primers

value: delta_uppY mutant alone


title: T2C_ArcC5GFAP_M1

value: Arctic mouse model of ADtic mice overexpressing C5a under the GFAP promoter


title: T2H_C5GFAP_M1

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole hippocampus. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).

value: WT mice overexpressing C5a under the GFAP promoter


title: T2C_C5GFAP_M1


title: UPP Pathway Specific Mutants 1_S94

description:
GSF1768.S94.PoolTn-Seq
Illumina sequenced using transposon specific primers

value: 2 Bar-coded parent genotypes delta_uppY and delta_uppW


title: Tumor Patient 1

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK006-1


title: Tumor Patient 9

description:
Samples are 4 matched tissue from the same patients with 16 total patients
LK114-1


title: LacZ_RNAi_Rep1_PRO

city: Baton Rouge

first: Craig

last: Hart

state: Louisiana

address: Life Science Building, LSU

department: Biological Sciences

institute: Louisiana State University

data_processing:
Library strategy: PRO-seq
Libraries were sequenced by the Cornell Biotechnology Resource Center on an Illumina NextSeq 500. The six bar-coded PRO-seq libraries (biological replicates of the 3 RNAi treatments) were pooled and 75 nucleotide reads were obtained. The six bar-coded MNase-seq libraries were pooled and 2 x 32 nucleotide paired-end reads were obtained.
Fastq was aligned to the Drosophila melanogaster dm3 reference genome with up to 2 mismatches using Bowtie (LANGMEAD 2010)  Parameters: bowtie -p9 -v2 -M1 -q --sam
PRO-seq Fastq files were processed using the FastX toolkit (hannonlab.cshl.edu/fastx_toolkit/index.html) to filter, clip the Illumina adapters (fastx_clipper), trim to 26-mers (fastx_trimmer), and aligned to the Drosophila melanogaster dm3 reference genome with up to 2 mismatches using Bowtie (LANGMEAD 2010).  Parameters: bowtie -p9 -v2 -M1 -q --sam
PRO-seq reads correspond to the sense strand of RNA, so were converted to their reverse complement before alignment. A summary of sequencing yields and the number of reads that uniquely mapped to the genome is given in Supplemental Table 2. Replicates were highly correlated (Supplemental Figure 1) and combined for further analyses except for DESeq2. Sequence data were deposited at NCBI Gene Express Omnibus (GEO) under accession number xxxxxx. Using a list of 9452 non-overlapping genes (CORE et al. 2012), custom scripts were used with PRO-seq data to count promoter-proximal (50 bp window with the most reads from -50 to 150 relative to the annotated TSS) and gene body (from 200 bp downstream of the TSS to 200 bp upstream of the annotated gene end) Pol II sequence reads and to calculate pausing indexes.
Custom scripts: https://github.com/McKowen-JK/BEAF_Pbro
Genome_build: dm3
Supplementary_files_format_and_content: bigwig, DESeq2 results

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cell tissue culture and RNAi treatment Drosophila S2 cells were grown at 25⁰C in M3 + BPYE medium with 10% fetal bovine serum (FBS) and antibiotic/antimycotic (anti/anti; 100 U/ml penicillin, 0.1 mg/ml streptomycin, 250 ng/ml amphotericin B) from 5 x 10e5 to 10e7 cells/ml.

extract_protocol:
Nuclei were isolated as in (KWAK et al. 2013)
PRO-seq library preparation: Nuclei were isolated and PRO-seq libraries were prepared as previously described using 10 PCR cycles after adaptor addition and reverse transcription (KWAK et al. 2013; MAHAT et al. 2016).

treatment_protocol: Cells at 5 x 10 6 cells/ml were diluted 5- fold with serum-free M3 + BPYE + anti/anti and 150 μg dsRNA was added to 15 ml cells in T150 flasks. After incubating 45 min at 25⁰C, 15 ml of the same medium supplemented with 20% FBS was added to the cells. After 2.5 days another 150 μg dsRNA was added followed by 30 ml M3 + BPYE, anti/anti and 10% FBS, and the cells were split into two new flasks. After another 2.5 days the cells were harvested for isolation of nuclei. Synthesis of dsRNA used a dsDNA template with a T7 RNA polymerase promoter on both ends. The dsRNA was 668 bp for BEAF, 493 bp for Pbro, and 835 bp for LacZ. The DNA templates were generated by PCR using the following primers: BEAF forward (CTAATACGACTCACTATAGGGAGCAAGGCCAAGACGCTGAG); BEAF reverse (CTAATACGACTCACTATAGGGAGCGCTGATTTGCCCATTTAC); Pbro forward (CTAATACGACTCACTATAGGGAGCACTACTACGACATTATCAGGG); Pbro reverse (CTAATACGACTCACTATAGGGAGCTCTGTGCGGGACAACTTTC); control LacZ forward (GAATTAATACGACTCACTATAGGGAGAGATATCCTGCTGATGAAGC); LacZ reverse (GAATTAATACGACTCACTATAGGGAGAGCAGGAGCTCGTTATCGC).

tag: RNAi

value: LacZ


title: T2H_ArcC5KO_F1

tag: Sex

value: Arctic mouse model of ADtic mice with C5ar1 knocked out (constitutive KO)


title: LacZ_RNAi_Rep2_PRO


title: UPP Pathway Specific Mutants 1_S93

description:
GSF1768.S93.PoolTn-Seq
Illumina sequenced using transposon specific primers

tag: genotype


title: T2C_ArcC5KO_F1


title: BEAF_RNAi_Rep2_PRO

value: BEAF


title: T2H_C5KO_F1

value: Female

value: WT mice with C5ar1 knocked out (constitutive KO)


title: P2336_N701-S516

value: epitheloid cervix carcinoma cell line

tag: cell line

value: HeLa (ATCC CCL-2)


title: Pbro_RNAi_Rep1_PRO

value: polybromo


title: T2H_Arc_M1

value: Male

value: 2 months

value: Arc

value: Arctic mouse model of AD


title: T2C_C5KO_F1


title: LacZ_RNAi_Rep2_MNase

data_processing:
Libraries were sequenced by the Cornell Biotechnology Resource Center on an Illumina NextSeq 500. The six bar-coded MNase-seq libraries (biological replicates of the 3 RNAi treatments) were pooled and 2 x 32 nucleotide paired-end reads were obtained.
MNase-seq (paired-end) Fastq files were processed using the FastX toolkit (hannonlab.cshl.edu/fastx_toolkit/index.html) to filter, clip the Illumina adapters (fastx_clipper), trim to 26-mers (fastx_trimmer), and align to the Drosophila melanogaster dm3 reference genome with Bowtie2
bowtie2 -p 8 -X 250 --no-discordant --no-mixed –no-unal
Custom scripts were used with MNase-seq data to select 120 to 180 bp DNA fragments and calculate nucleosome centers. Nucleosome centers were used to create 50bp pseudo-fragments before converting to bigWig. Nucleosome centers were used to create 50bp pseudo-fragments before converting to bigwig.
Custom scripts: https://github.com/McKowen-JK/BEAF_Pbro
Genome_build: dm3
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells were treated with 1% formaldehyde for 2 min at room temperature, and cross- linking was quenched by adding glycine to 125 mM and placing the cells on ice. Nuclei were isolated as for PRO-seq (KWAK et al. 2013), except they were stored in MD buffer (10 mM Tris- HCl pH 8.0, 250 mM sucrose, 1 mM CaCl 2, 60 mM KCl, 15 mM NaCl, 1 mM DTT).
MNase digestions were done in 140 μl MD buffer on nuclei from 1.5 x 10e7 cells with 4000 U MNase (NEB gel units) at room temperature for 30 min, resulting in around 90% mononucleosomes. Reactions were stopped (360 μl 142 mM NaHCO 3, 1.42% SDS, 350 mM NaCl, 17.5 mM EDTA, 2.8 mM EGTA), DNA was isolated, and MNase-seq libraries were prepared as previously described (WEI et al. 2012). After 4 PCR cycles, DNA in the size range of 80 to 220 bp (not including adapter sequences) was isolated and sequenced.

tag: sirna


title: T2H_ArcC5GFAP_M1


title: Nodular goiters, biological replicate 5

city: Hangzhou

first: Lisong

last: Teng

address: Yuhangtang Road

institute: Zhejiang University

description:
Gene expression data from nodular goiter
N5

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

data_processing: The raw data were normalized by Expression Console software of Affymetrix company.

source_name: Nodular goiters

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix  WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US)/ Ovation FFPE WTA System (Cat#3403， NuGEN, San Carlos, CA, US) and FL-Ovation™ cDNA Biotin Module V2(Cat#4200， NuGEN, San Carlos, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

extract_protocol: Total RNA was extracted and purified using RecoverAllTM  Total Nucleic Acid Isolation (Cat#AM1975, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: All tissue samples were retrieved from formalin-fixed paraffin-embedded blocks and reviewed by an experienced attending pathologist

tag: disease state

value: Nodular goiters

value: Thyroid


title: Nodular goiters, biological replicate 6

description:
Gene expression data from nodular goiter
N6


title: Nodular goiters, biological replicate 4

description:
Gene expression data from nodular goiter
N4


title: Nodular goiters, biological replicate 3

description:
Gene expression data from nodular goiter
N3


title: T2H_WT_M1

value: WT

value: Wild type


title: Nodular goiters, biological replicate 2

description:
Gene expression data from nodular goiter
N2


title: BEAF_RNAi_Rep2_MNase


title: UPP Pathway Specific Mutants 3_S61

description:
GSF1944.S61.PoolTn-Seq
Illumina sequenced using transposon specific primers

value: delta_uppW mutant alone


title: Fibp_2_KO

city: Bethesda

first: Peng

last: Jiang

state: Maryland

address: 41 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt version 1.18. The read alignment used the STAR version 2.7.0f  with the reference genome (Mouse - mm10) using Ensemb version 96 (Gencode M21) GTF annotation.
The gene expression quantification analysis was performed for all samples using RSEM version 1.3.1
The differential expression analysis was performed between Fibp and Rosa26 knockouts using the DESeq2 1.30.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes count values for each sample.
Supplementary_files_format_and_content: tab-delimited text file includes differential expression values between Fibp and Rosa26 knockouts.

source_name: spleen

growth_protocol: Cells were cultured in completed RPMI 1640 medium, which is RPMI 1640 Medium (Gibco, 11875119) supplemented with 10% inactivated fetal bovine serum (Gibco, 10082147), 20 mM HEPES (Gibo, 15630080), 1 mM sodium pyruvate (Gibco, 11360070), 50uM 2-mercaptoethanol (Gibco, 21985023), 2 mM L-glutamine (Gibco, 25030024), and 1% Penicillin-Streptomycin (P/S, Gibco, 15140122) at 1x10E6 cells/mL.

extract_protocol:
CD8+ T cells were isolated from the single-cell suspension of splenocytes of Pmel-1 TCR transgenic mice using the EasySep mouse CD8+ T cell isolation kit (STEMCELL, Cat# 19853) by magnetic negative selection. If cells were not used directly, the freshly isolated splenocytes would be frozen in cryopreservation medium (Gibco, Cat# 2176664). CD8+ T cells isolated from newly-thawed splenocytes using the same method were rested in the medium overnight before stimulation. Isolated CD8+ T cells were stimulated with plate-bound anti-mouse CD3 (TONBO, 40-0032-U100, clone 17A2) at 10 ug/mL and anti-mouse CD28 (TONBO, 40-0281-U100, clone 37.51) at 5 ug/mL for 48 hours before expanded with recombinant mouse IL-2 (Biolegend, 575406) at 100 IU/mL.
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded mRNA-seq library protocol

tag: strain

value: Pmel1 transgenic

tag: knockout condition

value: Fibp KO

value: spleen

value: CD8 T cells


title: Fibp_3_KO

tag: tissue


title: T2C_Arc_M1

description: Mice were perfused with PBS and cortex and hippocampus were dissected. RNA was extracted from whole cortex. Bulk RNA-seq protocol was performed as previously described (Mortazavi et al.  2008).


title: Nodular goiters, biological replicate 1

description:
Gene expression data from nodular goiter
N1


title: LacZ_RNAi_Rep1_MNase

value: LacZ


title: BEAF_RNAi_Rep1_MNase

value: BEAF


title: Fibp_1_KO


title: T2C_WT_M1


title: Pbro_RNAi_Rep1_MNase


title: Pbro_RNAi_Rep2_PRO


title: BEAF_RNAi_Rep1_PRO


title: Follicular thyroid carcinoma, biological replicate 1

description:
Gene expression data from FTC
FTC1

source_name: Follicular thyroid carcinoma

value: Follicular thyroid carcinoma


title: Rosa26_2_KO

value: Rosa26 KO


title: Follicular thyroid carcinoma, biological replicate 4

description:
Gene expression data from FTC
FTC4


title: WT-GFP_Cu rep3 (B3)

city: Duarte

first: Cai

last: Hongxia

state: California

address: 1500E Duarte Rd

institute: City of hope Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v 2.2.1.0 with parameters --rna-strandness rf --fr.
Fragments Per kb Per Million Reads of library size (FPKM) were calculated using a protocol from Adam et al., Genome Biology, 2011. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: reprogrammed hepatocytes

growth_protocol: Primary hepatocytes from ATP7B-/- or WT mice were reprogrammed with 20 ng/ml HGF and EGF, 10uM Y-27632, 10uM A8301, 3uM CHIR99021,1uM S1P and 5uM LPA to become liver progenitors. After lentivirus ATP7B or GFP transduction and rediffierentiation (20ng/ml OSM, 10uM DAPT and SB431542) for 3 weeks, KO-ATP7B-Heps, KO-GFP-Heps, and WT-ATP7B-Heps were treated with 100 uM CuCl2 for 24 hours.

extract_protocol:
All cells were washed by PBS and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All replicates were100 uM CuCl2 treated for 24 hours.

value: liver progenitor cell redifferentiated hepatocytes

tag: treatment

value: 100 mM CuCl2


title: WT-GFP_Cu rep1 (B1)


title: Pbro_RNAi_Rep2_MNase

value: polybromo


title: Follicular thyroid carcinoma, biological replicate 3

description:
Gene expression data from FTC
FTC3


title: Rosa26_3_KO


title: Rosa26_1_KO


title: KO-GFP_Cu rep3 (D3)


title: DglnA3_1mM Mn

city: Chandigarh

first: Dipak

last: Dutta

email: dutta@imtech.res.in, ddutta25@gmail.com

state: Chandigarh

address: Sector 39-A

department: Molecular Biochemistry

country: India

institute: CSIR IMTECH

description: Gene expression_DglnA strain_Plus manganase_3

hyb_protocol: 2000ng ng of labeled cRNA sample were fragmented at 60° C and hybridized on to a Agilent custom Microarray Gene expression 8x15k Array (AMADID: 068043). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using in-house coded R Scripts (https://cran.r-project.org/). Normalization of the data was done in R-Scripts .

organism: Escherichia coli

source_name: Bacteria_LB+1mM Mn grown

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligodT primer with T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Overnight cultures of E. coli strains were inoculated in the fresh LB medium at 1:100 dilution and grown initially for 1 hour to get the O.D. about 0.3 and then grown again for 2.5 hours in the presence or absence of 1 mM manganese at 37°C. 2.5 ml stop solution (5% phenol in ethanol) was added in 25 ml of growing culture for 10 minutes to prevent the RNA degradation and the cell pellets were collected by centrifuging at 5000 rpm for 10 minutes at 4°C. The pellets were washed with normal saline (0.9%) and stored by dissolving in 600ml RLT buffer before further processing.

extract_protocol: RNA Extraction was perforemd using Qiagen RNeasy Mini kit (Cat. No. 74106) as per the manufacturer's recommendations.

treatment_protocol: The cells were grown in the presence or absence of 1 mM of manganese for 2.5 hours at 37°C

value: deltaglnA


title: Parental

value: Parental


title: DglnA2_1mM Mn

description: Gene expression_DglnA strain_Plus manganase_2


title: WT-GFP_Cu rep2 (B2)


title: KO-GFP_Cu rep2 (D2)


title: KO-ATP7B_Cu rep2 (C2)


title: CC2 iPSC-CMs

city: Baltimore

first: Matthew

last: Miyamoto

state: MD

address: 670 W Baltimore St

department: Cardiology

institute: University of Maryland Medical Center

data_processing: Mapping was done using CellRanger with human reference.

source_name: Cardiomyocytes

growth_protocol: We generated iPSC derived CMs using established GiWi CM differentiation protocols. CMs were purified using metabolic seletection

extract_protocol:
On D35 CMs were dissociated and captured using conventional 10x chromium controller.
We generated libraries using the 10x chromium platform and sequenced on a Novaseq S4 Flow cell

treatment_protocol: Both lines were differentiated and matured using the identical protocols (metabolic selection, T3+Dex maturation_

value: iPSC derived Cardiomyocytes

tag: condition

value: control


title: KO-GFP_Cu rep1 (D1)


title: cDCM iPSC-CMs

value: congenital dilated cardiomyopathy (cDCM)


title: DmntPDglnA2

description: Gene expression_DmntPDglnA strain__minus manganase_2

source_name: Bacteria_LB grown

value: deltamntPdeltaglnA


title: KO-ATP7B_Cu rep3 (C3)


title: DmntPDglnA2_1mM Mn

description: Gene expression_DmntPDglnA strain_Plus manganase_2


title: DglnA1_1mM Mn

description: Gene expression_DglnA strain_Plus manganase_1


title: HOMO-2: E18 Csmd3-/- cortex rep2

city: Beijing

first: Wei

last: Song

address: 1 Beichen West Road, Chaoyang District

institute: Beijing Institutes of Life Science, CAS

data_processing:
Raw data quality control was performed using FastQC(v0.11.9)
Adaptors and low-quality reads were removed using trim_galore(v0.4.4)
Clean reads were aligned to reference genome  using hisat2(v2.0.5)
Transcript assembly and read counts extraction were performed using StringTie  (v1.3.4) and prepDE.py
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cortex

growth_protocol: After copulation was observed between Csmd3 heterzygous mice, the female mice were separated and the embryo were obtained at 18 days post cocopulation.

extract_protocol:
RNA was extracted from  embryonic 18 days by TRIzol method. Then, total RNA was quantiﬁed and quality controlled by Agilent Bioanalyzer 2100 system . And 500ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: cortex

tag: development stage

value: Csmd3 knockout


title: WT-3: E18 WT cortex rep3

value: WT


title: DmntPDglnA3

description: Gene expression_DmntPDglnA strain_minus manganase_3


title: KO-ATP7B_Cu rep1 (C1)


title: DglnA2

description: Gene expression_DglnA strain_minus manganase_2


title: WT2

description: Gene expression_Wild Type strain_minus manganase_2


title: HOMO-3: E18 Csmd3-/- cortex rep3


title: Follicular thyroid carcinoma, biological replicate 2

description:
Gene expression data from FTC
FTC2

value: Thyroid


title: HOMO-1: E18 Csmd3-/- cortex rep1


title: 40478_V1

status: Public on Mar 04 2022

city: Los Angeles

first: Katherine

last: Eyring

address: 695 Charles E. Young Dr. South

institute: UCLA

description: con

data_processing:
Reads were mapped to the macaque genome (rheMac8) using the STAR (Spliced Transcripts Alignment to a Reference) aligner, and gene-level quantifica- tions were calculated with Kallisto (Pachter Lab, Pasadena, CA)
Using the filterByExpr method from the R package edgeR, 6410 lowly expressed genes were filtered and removed and were highly enriched for olfactory receptors and ribosome related genes
Samples under- went trimmed mean of M values normalization for read depth followed by differential gene expression with Limma-voom. Sequencing metrics from Picard tools were summarized by their top four principal components (seqPCs), which were included in the linear model to control for batch, RNA quality, and sequencing-related tech- nical effects.
The following model was used, with specific contrast terms to determine differential gene expression between different indi- vidual regions: Expr ~ 0 +  Group:Region + seqPCs1-4. p Values were then corrected for multiple comparisons using the fdrtool package in R (R version 3.6.0; the R Foundation, Vienna, Austria).
Genome_build: rheMac8
Supplementary_files_format_and_content: The Table_S2_LogFC.xlsx file contains the output of limma-voom DGE analysis (model above)
Supplementary_files_format_and_content: The Table_S4_LogFC.xlsx file contains the data used for the WGCNA analysis

organism: Macaca mulatta

source_name: NHP

growth_protocol: All animal protocols were developed in conjunction with the California National Primate Research Center and approved by the University of California, Davis Institutional Animal Care and Use Committee. Thirteen female rhesus macaques were split into three treatment conditions: immune activation dur- ing the first trimester of pregnancy (first-trimester MIA, n = 5), immune activation during the second trimester of pregnancy (second-trimester MIA, n = 4), or control (n = 4). At 3.5 to 4 years of age, four brain regions were dissected from the right hemisphere: the dorsolateral prefrontal cortex (DLPFC) (Brodmann area 9/46) on the middle frontal gyrus along the dorsal wall of the principal sulcus, anterior cingulate cortex (ACC) (Brodmann area 24), mid-rostrocaudal hippo- campus (HC) caudal to the amygdala, and primary visual cortex (V1).

extract_protocol:
RNA was extracted (miRNeasy Mini; Qiagen, Hilden, Ger- many), and ribosomal RNA-depleted RNA-seq libraries were prepared using TruSeq Stranded RNA Plus Ribo-Zero Gold kits (Illumina, Inc., San Diego, CA).
Libraries were multiplexed (24 per pool) and sequenced across two batches on an Illumina HiSeq2500 to an average depth of approximately 50 million 69 bp paired end reads.
bulk RNAseq

treatment_protocol: The control group consisted of one untreated, one first trimester saline- injected, and two second trimester saline-injected NHPs. Animals in the MIA conditions were injected intravenously with 0.25 mg/kg synthetic double-stranded RNA virus (pol- y:ICLC) (Oncovir, Inc., Washington, DC) on gestational days 43, 44, and 46 (first-trimester MIA) or 100, 101, and 103 (second-trimester MIA).

tag: brain region

value: CON


title: DmntPDglnA1_1mM Mn

description: Gene expression_DmntPDglnA strain_Plus manganase_1


title: 40390_HC

value: HC

value: MIA


title: 40390_DLPFC

value: DLPFC


title: 40390_V1


title: 40482_V1

description: con


title: WT-1: E18 WT cortex rep1


title: 40390_ACC

value: ACC


title: 40360_V1


title: 40482_HC

description: con


title: 40482_ACC

description: con


title: DglnA1

description: Gene expression_DDglnA strain_minus manganase_1


title: 40360_HC


title: WT1

description: Gene expression_Wild Type strain_minus manganase_1


title: DmntPDglnA1

description: Gene expression_DmntPDglnA strain_minus manganase_1


title: 40478_HC

description: con


title: 40478_DLPFC

description: con


title: 40360_ACC


title: 40478_ACC

description: con


title: 40335_HC

description: con


title: DmntPDglnA3_1mM Mn

description: Gene expression_DmntPDglnA strain_Plus manganase_3


title: 40335_V1

description: con


title: 40318_V1


title: 40335_ACC

description: con


title: WT-2: E18 WT cortex rep2


title: 40335_DLPFC

description: con


title: 40482_DLPFC

description: con


title: 40318_HC


title: 40318_ACC


title: WT_1mM Mn

description: Gene expression_Wild Type strain_plus manganase_1


title: 40302_DLPFC


title: 40302_V1


title: 40302_HC


title: 40302_ACC


title: 40295_HC

description: con


title: 40212_HC


title: 40295_DLPFC

description: con


title: 40295_V1

description: con


title: 40212_V1


title: 39988_V1


title: 39988_DLPFC


title: 39827_DLPFC


title: 39988_HC


title: 40360_DLPFC


title: 40295_ACC

description: con


title: 40212_DLPFC


title: 39813_ACC


title: 39813_DLPFC


title: 39988_ACC


title: 39673_HC


title: 39673_ACC


title: 39673_DLPFC


title: 40318_DLPFC


title: Neurons+sAPPa-T0h, rep3

city: Dunedin

first: Katie

last: Peppercorn

state: Otago

address: 710 Cumberland Street

country: New Zealand

institute: University of Otago

data_processing:
FastQ files were trimmed by Trimmomatic - sliding window 4:20 (average over 4 bases, minimum read quality 20)
STAR function 'Genome generate' created a genome index with the GRCh38 genome sequences.
STAR align function 'alignReads' aligned the reads to the GRCh38 genome sequences and generated BAM files.
Samtools 'merge' function merged the BAM files for each read pair and lane (flow cell)
MultiQC generated a quality control report of the sequence data
FeatureCounts tool from the Subread package was used to generate the read count table
Functions of limma and EdgeR were used to perform differential expression analysis and statistics
Genome_build: Alignment was to the human genome GRCh38
Supplementary_files_format_and_content: Read count table generated from merged BAM files. File contains gene ID, chromosome number, number of reads, length of reads for each sample.

source_name: iPSC-derived glutamatergic neurons

growth_protocol: iPSCs were cultured on Matrigel coated 100mm cell culture dishes and differentiation into glutamatergic neurons was induced by the addition of 10 uM doxycycline to the culture media for three days after which cells were plated on poly L ornathine coated 6 well plates in cortical media (Brain Phys neuronal media (STEM cell technologies), 1x B27 suppliment (GIBCO) 10ng/mL BDNF (Preprotech) in PBS containing 0.1% (w/v) IgG and protease free BSA, 1 mg/mL laminin (GIBCO)). Half media changes every 3 days for the first week followed by half media change 1 x week. Reference for this cell culture method - Fernandopulle et al. (2018). Transcription-factor mediated differentiation of human iPSCa into neurons. Current Protocols in Cell Biology 79, e51. doi 10/1002/cpcb.51.

extract_protocol:
350 mL lysis buffer RL (Norgen total RNA extraction kit) was added directly to each well and the RNA extracted following manufacturers protocol. DNA was removed by DNAse treatment and purification on an RNA clean up kit (Zymogen). Integrity of RNA was assessed on a bioanalyser and all samples were RIN/RQN = >9.5.
Libraries were prepared using TruSeq Stranded Total RNA library  Prep Gold Kit (Illumina Inc, San Diago, USA). Each library was uniquely indexed and validated according to the manufacturers protocol. The 9 pooled libraries at equimolar concentrations were then paired end sequenced across four lanes of HiSeq 2500 flow cells using V2 Rapid chemistry (Illumina) generating 100 bp reads.
RNA-seq / ribo depletion

treatment_protocol: At DIV 18 sAPPa was added to the cells in a reverse time course (2 h, 30 min or 0 h) so that at time of harvesting all cells had been in culture for the same time.

value: iPSC cells genetically modified to express transcription factor NGN2 after exposure to doxycycline

value: iPSC-derived glutamatergic neurons

value: 0 h exposure to sAPPa protein


title: Neurons+sAPPa-T0h, rep1


title: Neurons+sAPPa-T05h, rep2

value: 0.5 h exposure to 1 nM sAPPa protein


title: Neurons+sAPPa-T05h, rep1


title: Neurons+sAPPa-T2h, rep3

value: 2 h exposure to 1 nM sAPPa protein


title: 39813_HC


title: Kasumi1_Input

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie2 v2.2.6.
Peaks were called using MACS2
RPKM normalized bigwig files were generated using Deeptools 3.1.2
Genome_build: hg19
Supplementary_files_format_and_content: RPKM normalized bigwig files were generated using Deeptools 3.1.2, reads were elongated to 250bp

source_name: hematopoietic cells

extract_protocol:
Cells were fixed in 1% formaldehyde, chromatine was sonicated using a Bioruptor Pico
Libraries were constructed using a custom protocol and NEXTFLEX adapters and barcodes

value: Kasumi1 cell line

tag: antibody

value: sonicated Input chromatin


title: 40212_ACC


title: Myotubes, 12-10NH

city: Waco

first: Panagiotis

last: Koutakis

state: TX

address: 101 Bagby Ave

institute: Baylor University

data_processing:
HISAT2 was used to map reads to the human transcriptome Gencode v. hg39 p.13 with default parameters
Cuffdiff was used to perform differential expression analysis with the reference human transcriptome Gencode v. hg39 p.13 using the following parameters: Library Normalization Method: Geometric, Dispersion Estimation Method: Blind, Library Prep used for input reads: ff-firststrand
Genome_build: hg38 p.13
Supplementary_files_format_and_content: Comma separated values text file with normalized abundance measurments and differential expression calculations

source_name: Myotubes

growth_protocol: Primary human skeletal muscle cells (SkMCs) derived from a PAD patient (Cook Myosite, Pittsburgh, PA, SK-1111) were cultured at 37°C under standard cell culture conditions (20% O2, 5% CO2). Culture medium consisted of Ham’s F-10 Nutrient Mixture, 20% fetal bovine serum (FBS), 1% Penicillin-Streptomycin (Pen-Strep) solution (Thermo Fisher, 11550-043, 26140-079, 15140-122), and 5 ng/mL Fibroblast Growth Factor-basic (FGF-b) (Sigma-Aldrich, St. Louis, MO, GF003). Skeletal Muscle Cells were developed into myotubes by incubating for 4 days with MyoTonic Differentiation Media (Cook Myosite, Pittsburgh, PA, MD-5555)

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (Qiagen) per manufacturer instructions.
Library construction was performed by Genewiz Inc. according to their poly-A selection protocol.

treatment_protocol: Cell were grown in either normoxic conditions (20% O2) or under conditions of cycling, NH: 90 min at normoxia (N) (20% O2, 75% N2, 5% CO2) and 90 min at hypoxia (1% O2, 94% N2, 5% CO2), NHH: 90 min at N, 60 min at hypoxia, and 30 min at hyperoxia (30% O2, 65% N2, 5% CO2).

tag: cell type

value: Skeletal Muscle Derived Cells (Cook Myosite)

value: Myotubes

value: Normoxia/Hypoxia Cycling

value: Peripheral Artery Disease (PAD) Patient

tag: individual


title: 39827_HC


title: Myotubes, 60NH


title: Myotubes, 74NHH

value: Normoxia/Hypoxia/Hyperoxia Cycling

value: Control Patient


title: Myotubes, 74NH


title: 39673_V1


title: 39813_V1


title: Myotubes, 74N

value: Normoxia


title: Neurons+sAPPa-T05h, rep3


title: Blood donor #11, PBMCs HTO

city: Berlin

first: Dylan

last: Postmus

state: Berlin

address: Charitépl. 1

department: Institute of Virology

institute: Charité – Universitätsmedizin Berlin

data_processing:
FASTQ files from RNA-seq library sequencing were processed using the Cell Ranger pipeline v 3.1.0 (10X Genomics)
FASTQ files from HTO classification library sequencing were processed using the CITE-seq-Count (Patrick Roelli, bbimber, Bill Flynn, santiagorevale, & Gege Gui. (2019). Hoohm/CITE-seq-Count: 1.4.2 (1.4.2). Zenodo. https://doi.org/10.5281/zenodo.2590196). Each cell barcode was allocated to the different treatments based on the enrichment of the HTO oligo assigned to each treatment (Mock: GGTTGCCAGATGTCA; SARS-CoV: CAGTAGTCACGGTCA; SARS-CoV-2: CTCCTCTGCAATTAC) associated with that barcode.
Cell Ranger output was further analysed by using Seurat v3.1.4 package (Butler et al. 2018) in R v3.6 (https://www.r-project.org/). Code available at https://github.com/GoffinetLab/SARS-CoV-2_PBMC-study.
Reads were also aligned to the two SARS-CoV/SARS-CoV-2 genomes (AY310120.1 and NC_045512.2) using the same CellRanger pipeline.
Genome_build: hg38 (human read alignment)
Genome_build: SARS-CoV AY310120.1 (Genbank)
Genome_build: SARS-CoV-2 NC_045512.2 (Genbank)
Supplementary_files_format_and_content: Seurat R object

source_name: Blood

growth_protocol: Human PBMCs were isolated from buffy coats by Ficoll-Hypaque centrifugation. PBMCs were cultured at 2 × 106/ml in RPMI 1640 containing 10% heat-inactivated fetal calf serum (Sigma-Aldrich), 1% penicillin-streptomycin (Thermo Fisher Scientific) and 2 mM L-glutamine (Thermo Fisher Scientific).

extract_protocol:
Samples were multiplexed using TotalSeq-A Antibodies purchased from BioLegend (A0256, A0258 and A0259). Antibody staining and the subsequent library preparation were performed following manufacturer’s instructions. Each treatment was assigned (and stained with) an HTO oligo, which is conjugated to a mixture of antibodies against ubiquitously expressed mammalian cell surface markers. This allows for demultiplexing of samples following sequencing based on HTO oligo enrichment for each cell barcode. The allocated HTO oligos were as follows: Mock: GGTTGCCAGATGTCA; SARS-CoV: CAGTAGTCACGGTCA; SARS-CoV-2: CTCCTCTGCAATTAC.
Single-Cell RNA-seq libraries were prepared with the 10x Genomics platform using the Chromium Next GEM Single Cell 3’ Reagent Kits v.3.1 following manufacturer’s instructions.
Single-Cell RNA-seq libraries were prepared with the 10x Genomics platform using the Chromium Next GEM Single Cell 3’ Reagent Kits v.3.1 following manufacturer’s instructions. Quality control of the libraries were performed with the KAPA Library Quantification Kit and Agilent TapeStation
HTO classification libraries were constructed using the TotalSeq-A kit (Biolegend; A0256, A0258 and A0259) following manufacturer's instructions. Sample HTO oligo multiplexing was as follows: Mock: GGTTGCCAGATGTCA; SARS-CoV: CAGTAGTCACGGTCA; SARS-CoV-2: CTCCTCTGCAATTAC.

treatment_protocol: Virus challenge occurred by inoculation of 0.4 x 106 cells/ml in RPMI cell culture medium supplemented with 2% FCS. Four hours post-challenge, cells were centrifuged and supernatants were collected (referred to as inoculum). Cells were resuspended in RPMI cell culture medium supplemented with 10% FCS and plated at 0.4 x 106 cell/1.5 ml in 12-wells.

value: Mock, SARS-CoV and SARS-CoV-2 exposed (multiplexed using TotalSeq-A Antibodies purchased from BioLegend (A0256, A0258 and A0259))


title: Blood donor #12, PBMCs used for single cell RNAseq

description: CG_JK_11-12_10x_stringent_sct_viralassign.rds


title: SUCCS1_WT_SOX10

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

institute: CHUV

data_processing:
The ChIPseq reads were first trimmed using Trimgalore
Trimmed reads were aligned on the human genome assembly hg19 with STAR version 2.5.0a, first taking all multiple matches for quality survey. Multiple matches, mitochondrial reads, as well as regions from the ENCODE Data Analysis Center (DAC) blacklisted regions (https://www.encodeproject.org/annotations/ENCSR636HFF/ , hg19 assembly) were then removed. A maximum of three redundant reads (i.e. reads with different IDs but mapping at the same genomic location) were kept for further analysis.
First, peaks were detected using MACS2 version 2.2.6 with an FDR of 1e-7 for ATF1_C and H3K4me3, and 1e-4 for EWSR1. In parallel, genomic enriched bins were extracted using the method described in : Renaud M, Praz V, Vieu E, Florens L, Washburn MP, L’Hôte P, et al. Gene duplication and neofunctionalization: POLR3G and POLR3GL. Genome Res. 2014;24: 37–51. 10.1101/gr.161570.113
To reduce the number of false-positives in the set, only the MACS2 peaks that intersected with the enriched genomic bins selected with the above-described method were considered for further analysis
CPM-normalized BigWig files were generated using bamCoverage (deepTools version 3.5.)
Genome_build: hg19
Supplementary_files_format_and_content: bibwig files for genome browser, and bed files with peaks positions

source_name: Cell line

growth_protocol: DTC1 and SUCCS1 were cultured in RPMI-1640 medium supplemented with 10% and 1% Pen/Strep as suspension cells in Ultra-low attachment flasks. HpMSCs were cultured in IMDM medium supplemented with 10%, 1% MEM NEAA, 1% Pen/Strep and 10 ng/ml PDGF-BB as adherent cells.

extract_protocol:
Cells were cross-linked with formaldehyde, flash-frozen and processed for ChIP using Protein G beads. ChIP DNA was purified with AMPure XP beads.
ChIP DNA libraries were prepared using the Illumina TruSeq ChIP library preparation kit (Illumina cat. no. IP-202-1012 or IP-202-1024) according to the manufacturer's instructions and 200-500 bp fragments selected using AMPureXP beads.

treatment_protocol: As indicated in the Samples “Treatment” column above

value: Derived from the pleural effusion of a 16 year old Caucasian girl with a heel CCS tumor

tag: chip antibody

value: SOX10 (PA5-40697, Invitrogen)

value: untreated

value: SU-CCS-1 ATCC CRL-2971


title: Kasumi1_H3K27ac_2

value: ChIP using anti-H3K227ac antibody


title: Neurons+sAPPa-T2h, rep1

value: iPSC cells genetically modified to express transcription factor NGN2 after exposure to doxycycline

value: iPSC-derived glutamatergic neurons


title: Kasumi1_H3K27ac_1

value: Kasumi1 cell line


title: 39827_V1

value: MIA


title: Myotubes, 60NHH

value: Skeletal Muscle Derived Cells (Cook Myosite)


title: Neurons+sAPPa-T2h, rep2

value: 2 h exposure to 1 nM sAPPa protein


title: SUCCS1_siEA_SOX10

value: Transfected with siRNA targeting EWSR1-ATF1 fusion transcript


title: SUCCS1_siEA_MITF

value: MITF (#91201, Active motif)


title: SUCCS1_siCTRL_TFAP2A

value: TFAP2A (sc-12726, Santa Cruz)

value: Transfected with CTRL siRNA


title: SUCCS1_siCTRL_MITF


title: SUCCS1_shCTRL_H3K27ac

value: H3K27ac (#39133, Active motif)

value: Infected with control shRNA targeting GFP transcript


title: SUCCS1_siCTRL_SOX10

value: Derived from the pleural effusion of a 16 year old Caucasian girl with a heel CCS tumor


title: Blood donor #11, PBMCs used for single cell RNAseq

value: Mock, SARS-CoV and SARS-CoV-2 exposed (multiplexed using TotalSeq-A Antibodies purchased from BioLegend (A0256, A0258 and A0259))


title: Blood donor #12, PBMCs HTO


title: SUCCS1_shATF1_H3K27ac

value: Infected with shRNA targeting wt ATF1 transcript


title: 39827_ACC

value: ACC


title: SUCCS1_shCTRL_ATF1_C

value: ATF1 C (LS-C351857, LS Bio)

value: SU-CCS-1 ATCC CRL-2971


title: Myotubes, 60N

value: Myotubes

value: Normoxia

value: Peripheral Artery Disease (PAD) Patient


title: Myotubes, 12-10N

value: Skeletal Muscle Derived Cells (Cook Myosite)


title: SUCCS1_shATF1_ATF1_C


title: SUCCS1_shATF1_ATF1_N

value: ATF1 N (A303-034A, Bethyl laboratories)


title: Neurons+sAPPa-T0h, rep2

value: iPSC cells genetically modified to express transcription factor NGN2 after exposure to doxycycline

value: iPSC-derived glutamatergic neurons

value: 0 h exposure to sAPPa protein


title: Myotubes, 12-10NHH

value: Normoxia/Hypoxia/Hyperoxia Cycling


title: SUCCS1_shCTRL_ATF1_N


title: SUCCS1_siEA_TFAP2A

value: TFAP2A (sc-12726, Santa Cruz)

value: Transfected with siRNA targeting EWSR1-ATF1 fusion transcript


title: DTC1_WT_SOX10

value: Derived from malignant pleural effusion of a patient with a chest wall CCS tumor

value: SOX10 (PA5-40697, Invitrogen)

value: untreated

value: DTC1 (CVCL_0J31)


title: ChIP-seq MCF-7 50nM CPI-1612 input DNA_rep2

first: David

last: Mayhew

state: MA

address: 500 Technology Square, Suite 700

institute: Foghorn Therapeutics

data_processing:
Illumina adapters (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT) were removed from the fastq files using Atropos (v1.1.28) {Didion, 2017}
Trimmed reads were mapped to the human reference GRCh38 using BWA mem v0.7.17 {Li, 2009} with default settings
Aligned bam files were filtered with bamtools {Barnett, 2011} to remove a) reads with more than 4 mismatches b) reads that are not in FR orientation within 2kb on the same chromosome.
PCR duplicate reads were removed using Picard v2.23.3 {Broad Institute}
Peaks of enrichment over input were identified using sample-matched input as a control with SICER2 v1.0.2 {Xu, 2014} with the gap size (-g) equal to 600 bp (-s hg38 -w 200 -rt 1 -f 150 -egf 0.74 -fdr 0.01 -g 600 -e 1000)
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig

growth_protocol: MCF-7 cells were grown in DMEM + 10%FBS at 37°C and 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation."
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500

treatment_protocol: Cells were treated with 50 nM CPI-1612 or DMSO for six hours.


title: ChIP-seq MCF-7 50nM CPI-1612 anti-H3K27ac_rep1


title: SUCCS1_WT_MITF

value: Derived from the pleural effusion of a 16 year old Caucasian girl with a heel CCS tumor

value: MITF (#91201, Active motif)


title: DTC1_WT_MITF


title: ChIP-seq MCF-7 50nM CPI-1612 anti-H3K9ac_rep2


title: ChIP-seq MCF-7 DMSO anti-H3K27ac_rep1

value: DMSO


title: ChIP-seq MCF-7 50nM CPI-1612 anti-H3K9ac_rep1


title: scATAC-seq MCF-7 DMSO

data_processing:
All raw base call (BCL) files generated by Illumina sequencers were converted to FASTQ files using cellranger-atac mkfastq function. Read filtering and alignment, barcode counting, and identification of transposase cut sites were detected using cellranger-atac count function (cellranger-atac_version 1.1.0) using the CellRanger reference package "refdata-cellranger-atac-GRCh38-1.1.0" with "gencode.v28.basic" annotations.
Cellranger-atac outputs were then processed with Signac v1.3 {Stuart, 2020} while filtering for peak_region_fragments > 3000 & peak_region_fragments < 20000 & pct_reads_in_peaks > 15 & blacklist_ratio < 0.05 & nucleosome_signal < 4 & TSS.enrichment > 2
DMSO and CPI-1612 samples were integrated with Harmony v1.0 {Korunsky, 2019} and transcription factor activity was calculated with chromVAR v1.12 {Schep, 2017} using the JASPAR2020 motif dataset.
Genome_build: GRCh38
Supplementary_files_format_and_content: Fragment files (.tsv.gz + .tsv.gz.tbi) and peak x barcode matrix files (.tsv + .mtx + .bed)

extract_protocol: Libraries were prepared with the 10X single-cell ATAC-seq protocol.


title: ChIP-seq MCF-7 DMSO input DNA_rep2


title: ChIP-seq MCF-7 DMSO input DNA_rep1


title: ChIP-seq MCF-7 DMSO anti-H3K9ac_rep2


title: RNA-seq ZR751 100nM Fulvestrant_rep3

description: RNAseq ZR751 ful_100nm-3

data_processing:
Isoform expression of Ensembl transcripts (GRCh38 release 99) was calculated with Salmon version 0.11.3 {Patro, 2017}.
Gene-level counts were then imported into R using tximport {Soneson, 2015}
Differential expression analysis was performed with DESeq2 v1.30.0  {Love, 2014} to analyze for differences between conditions, and the set of differentially expressed genes were filtered only for the genes with a |fold-change| of 1.5 and a Benjamini-Hochberg FDR adjusted P values less than or equal to 0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene-level counts as a csv

growth_protocol: Cells were grown in DMEM + 10%FBS at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted after 3 days using TRIzol (Invitrogen).
RNA-Seq analysis was performed with polyA selection and standard library construction

treatment_protocol: Cells were treated with CPI-1612 and/or Fulvestrant for six hours.

value: 100nM Fulvestrant


title: ChIP-seq MCF-7 50nM CPI-1612 anti-H3K27ac_rep2


title: ChIP-seq MCF-7 DMSO anti-H3K9ac_rep1


title: ChIP-seq MCF-7 DMSO anti-H3K27ac_rep2


title: RNA-seq ZR751 5nM CPI-1612_rep3

description: RNAseq ZR751 cpi_1612_5nm-3


title: RNA-seq ZR751 5nM CPI-1612 + 100nM Fulvestrant_rep3

description: RNAseq ZR751 cpi_1612_5nm_plus_ful_100nm-3

value: 5nM CPI-1612 + 100nM Fulvestrant


title: RNA-seq ZR751 50nM CPI-1612_rep3

description: RNAseq ZR751 cpi_1612_50nm-3


title: RNA-seq ZR751 100nM Fulvestrant_rep2

description: RNAseq ZR751 ful_100nm-2


title: RNA-seq ZR751 50nM CPI-1612 + 100nM Fulvestrant_rep2

description: RNAseq ZR751 cpi_1612_50nm_plus_ful_100nm-2

value: 50nM CPI-1612 + 100nM Fulvestrant


title: RNA-seq ZR751 5nM CPI-1612 + 100nM Fulvestrant_rep2

description: RNAseq ZR751 cpi_1612_5nm_plus_ful_100nm-2


title: RNA-seq ZR751 5nM CPI-1612_rep2

description: RNAseq ZR751 cpi_1612_5nm-2


title: RNA-seq ZR751 DMSO_rep3

description: RNAseq ZR751 dmso-3


title: RNA-seq ZR751 50nM CPI-1612_rep2

description: RNAseq ZR751 cpi_1612_50nm-2


title: RNA-seq ZR751 DMSO_rep2

description: RNAseq ZR751 dmso-2


title: scATAC-seq MCF-7 50nM CPI-1612


title: RNA-seq ZR751 100nM Fulvestrant_rep1

description: RNAseq ZR751 ful_100nm-1


title: RNA-seq ZR751 5nM CPI-1612_rep1

description: RNAseq ZR751 cpi_1612_5nm-1


title: RNA-seq T47D 50nM CPI-1612 + 100nM Fulvestrant_rep3

description: RNAseq T47D cpi_1612_50nm_plus_ful_100nm-3


title: RNA-seq T47D 50nM CPI-1612_rep3

description: RNAseq T47D cpi_1612_50nm-3


title: RNA-seq ZR751 50nM CPI-1612_rep1

description: RNAseq ZR751 cpi_1612_50nm-1


title: ChIP-seq MCF-7 50nM CPI-1612 input DNA_rep1


title: RNA-seq T47D 100nM Fulvestrant_rep3

description: RNAseq T47D ful_100nm-3


title: RNA-seq T47D 5nM CPI-1612 + 100nM Fulvestrant_rep3

description: RNAseq T47D cpi_1612_5nm_plus_ful_100nm-3


title: RNA-seq ZR751 DMSO_rep1

description: RNAseq ZR751 dmso-1


title: RNA-seq T47D 5nM CPI-1612 + 100nM Fulvestrant_rep2

description: RNAseq T47D cpi_1612_5nm_plus_ful_100nm-2


title: RNA-seq T47D 100nM Fulvestrant_rep2

description: RNAseq T47D ful_100nm-2


title: RNA-seq ZR751 50nM CPI-1612 + 100nM Fulvestrant_rep3

description: RNAseq ZR751 cpi_1612_50nm_plus_ful_100nm-3


title: RNA-seq T47D 50nM CPI-1612_rep2

description: RNAseq T47D cpi_1612_50nm-2


title: RNA-seq T47D DMSO_rep3

description: RNAseq T47D dmso-3


title: RNA-seq T47D 50nM CPI-1612 + 100nM Fulvestrant_rep1

description: RNAseq T47D cpi_1612_50nm_plus_ful_100nm-1


title: RNA-seq T47D 5nM CPI-1612_rep2

description: RNAseq T47D cpi_1612_5nm-2


title: RNA-seq T47D 5nM CPI-1612 + 100nM Fulvestrant_rep1

description: RNAseq T47D cpi_1612_5nm_plus_ful_100nm-1


title: RNA-seq T47D 50nM CPI-1612 + 100nM Fulvestrant_rep2

description: RNAseq T47D cpi_1612_50nm_plus_ful_100nm-2


title: RNA-seq T47D 50nM CPI-1612_rep1

description: RNAseq T47D cpi_1612_50nm-1


title: RNA-seq T47D DMSO_rep2

description: RNAseq T47D dmso-2


title: RNA-seq T47D 100nM Fulvestrant_rep1

description: RNAseq T47D ful_100nm-1


title: RNA-seq T47D 5nM CPI-1612_rep1

description: RNAseq T47D cpi_1612_5nm-1


title: RNA-seq MCF7 50nM CPI-1612 + 100nM Fulvestrant_rep3

description: RNAseq MCF7 cpi_1612_50nm_plus_ful_100nm-3


title: RNA-seq T47D DMSO_rep1

description: RNAseq T47D dmso-1


title: RNA-seq MCF7 5nM CPI-1612 + 100nM Fulvestrant_rep3

description: RNAseq MCF7 cpi_1612_5nm_plus_ful_100nm-3


title: RNA-seq MCF7 100nM Fulvestrant_rep3

description: RNAseq MCF7 ful_100nm-3


title: RNA-seq T47D 5nM CPI-1612_rep3

description: RNAseq T47D cpi_1612_5nm-3


title: RNA-seq ZR751 50nM CPI-1612 + 100nM Fulvestrant_rep1

description: RNAseq ZR751 cpi_1612_50nm_plus_ful_100nm-1


title: RNA-seq MCF7 50nM CPI-1612_rep3

description: RNAseq MCF7 cpi_1612_50nm-3


title: RNA-seq MCF7 DMSO_rep3

description: RNAseq MCF7 dmso-3


title: RNA-seq ZR751 5nM CPI-1612 + 100nM Fulvestrant_rep1

description: RNAseq ZR751 cpi_1612_5nm_plus_ful_100nm-1


title: RNA-seq MCF7 5nM CPI-1612_rep3

description: RNAseq MCF7 cpi_1612_5nm-3


title: RNA-seq MCF7 50nM CPI-1612 + 100nM Fulvestrant_rep2

description: RNAseq MCF7 cpi_1612_50nm_plus_ful_100nm-2


title: RNA-seq MCF7 5nM CPI-1612_rep2

description: RNAseq MCF7 cpi_1612_5nm-2


title: RNA-seq MCF7 50nM CPI-1612_rep2

description: RNAseq MCF7 cpi_1612_50nm-2


title: RNA-seq MCF7 100nM Fulvestrant_rep2

description: RNAseq MCF7 ful_100nm-2


title: RNA-seq MCF7 5nM CPI-1612 + 100nM Fulvestrant_rep2

description: RNAseq MCF7 cpi_1612_5nm_plus_ful_100nm-2


title: RNA-seq MCF7 DMSO_rep2

description: RNAseq MCF7 dmso-2


title: RNA-seq MCF7 5nM CPI-1612 + 100nM Fulvestrant_rep1

description: RNAseq MCF7 cpi_1612_5nm_plus_ful_100nm-1


title: RNA-seq MCF7 50nM CPI-1612 + 100nM Fulvestrant_rep1

description: RNAseq MCF7 cpi_1612_50nm_plus_ful_100nm-1


title: RNA-seq MCF7 100nM Fulvestrant_rep1

description: RNAseq MCF7 ful_100nm-1


title: RNA-seq MCF7 50nM CPI-1612_rep1

description: RNAseq MCF7 cpi_1612_50nm-1