title: HepG2-hNTCP HBV infected in the presence of Myrcludex B

city: Heidelberg

first: Yi

last: Ni

address: Im Neuenheimer Feld 344

department: Infectious Diseases

country: Germany

institute: University hospital Heidelberg

description:
10006031040_G_Grn
SAMPLE 9
Chip B

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Cells were grown in DMEM medium contain 10% FCS, 2 mM L-glutamine, 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: For infection, cells were inoculated with virus (day 0) overnight. On the next day (day 1) cells were washed 3 times with PBS. Then medium containing 2.5% DMSO were used to refresh cells every 2 days.

tag: infection

value: HBV (in the presence of Myrcludex B)

tag: time

value: day 9 post-infection

tag: infection rate

tag: parental cell line

tag: cell treated with 2% dmso before infection

value: No

tag: data presented in the manuscript

value: Yes

tag: rna

value: concentration (ng/ml):84.9


title: WT703M

status: Public on Jan 30 2018

type: SRA

city: Melbourne

first: Ashley

middle: P

last: Ng

state: Victoria

address: 1G Royal Parade, Parkville

department: Cancer and Haematology

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description:
sample name:
WT703M_C5LWPANXX_TCTCGCGC_L001

library_source: transcriptomic

data_processing:
Reads mapped to mm10 using Subjunc aligner in the Subread package
Read counts were summarised by featureCounts using NZCBI RefSeq gene annotation
Genes were filtered as not expressed if failed to achieve at least 0.5 counts per million reads in at least half the samples
Library sizes were normalised using the TMM method in voom software package converting read counts to log2 counts per million with associated precision weights
Differential expression was assessed using empirical Bayes moderated t-statistics that utilised the edgeR and limma software packages including batch in the linear model.
Genome_build: mm10
Supplementary_files_format_and_content: csv file with normalised counts

molecule: total RNA

organism: Mus musculus

source_name: LSK cells_MIG

growth_protocol: LSK cells (~100-200k/mouse) were extracted from tibia, femur and humuros bones from C57BL/6 mice (via FACS sorting), the transduced with either MIG or MIG-Hhex retrovirus (bound to retronectin coated plates) and cultured for two days (in StemPro-34 (Gibco) media with Nutrient Suppliment, P/S, L-Glutamine, 10ng/mL mL-3, 10ng/mL mIL-6, 50ng/mL mSCF and 50ng/mL mFlt-3).

extract_protocol:
Total RNA was extracted using RNAeasy Kit from Qiagen from GFP+ sorted LSK cells 2 days post-infection
Illumina - Library Prep mRNA. HiSeq HT chemistry- Single Read (50/100)  or xHiSeq HT chemistry- Paired Read (50/100)

tag: strain

tag: vector

value: MIG

tag: genotype

value: wild-type

tag: tissue

value: bone marrow

tag: cell type

value: LSK


title: HepG2-hNTCP not infected (10006031040_B_Grn)

type: RNA

description:
10006031040_B_Grn
SAMPLE 4
Chip B

label: biotin

organism: Homo sapiens

source_name: HepG2-hNTCP not infected

tag: cell line

value: concentration (ng/ml):93.8


title: HepG2-hNTCP not infected (10006031040_E_Grn)

description:
10006031040_E_Grn
SAMPLE 7
Chip B

value: concentration (ng/ml):67.2


title: SM_RNA_Conc1_R11

status: Public on Jan 31 2018

city: Utrecht

first: Michael

last: VanInsberghe

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: This is a sample of purified K562 RNA diluted to limiting dilution, then serially diluted by 5x, and assayed against GAPDH. Chip cell processing unit R11

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing: Raw CT values were normalized to the cut-off CT derived from the distribution of single-cDNA-molecule amplification events

label: FAM

source_name: K562 total RNA at limiting dilution

label_protocol: not applicable

growth_protocol: K562 cells were cultured in DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1× GlutaMAX (Gibco).

extract_protocol: Total RNA was isolated using the miRVana RNA isolation kit (Ambion) according to manufacturer directions, omitting the size-enrichment step

tag: dilution

value: 1× relative to highest concentration


title: HepG2-hNTCP HBV infected

description:
10006031040_F_Grn
SAMPLE 8
Chip B

source_name: HepG2-hNTCP HBV infected

value: HBV

value: concentration (ng/ml):89


title: HepG2-hNTCP HDV infected in the presence of Myrcludex B

description:
10006031040_D_Grn
SAMPLE 6
Chip B

value: HDV (in the presence of Myrcludex B)

value: concentration (ng/ml):101


title: HepG2-hNTCP HDV infected

description:
10006031040_C_Grn
SAMPLE 5
Chip B

source_name: HepG2-hNTCP HDV infected

value: HDV

value: concentration (ng/ml):42.7


title: M2_3

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

description:
SAMPLE 9
replicate 3

hyb_protocol: Standard Illumina hybridization protocol to HumanHT-12_v4_BeadChip arrays (Illumina, 15011977), following the Direct Hybridization Assay guideline.

scan_protocol: BeadChip Arrays were scanned with a HiScan Array Scanner (Illumina) using the iScan Control Software (Illumina).

data_processing: The data were normalised using quantile normalization implemented by the GenomeStudio Gene Expression Module v1.0 Software (Illumina).

label_protocol: 500 ng of each sample of RNA were processed to generate labeled cRNAs following the Illumina TotalPrep RNA amplification Kit (Ambion  #AMIL1791) protocol.

growth_protocol: hTERT-immortalized human mammary epithelial cells (IMECs) and IMEC-MYC were cultured at 37°C and 5% CO2 in 1:1 DMEM/F-12 medium (gibco #11320-074) supplemented with insulin (Clonetics, MEGM SingleQuots #CC-4136), EGF (Clonetics, MEGM SingleQuots #CC-4136), bovine pituitary extract (BPE) (Clonetics, MEGM SingleQuots #CC-4136) and hydrocortisone (Clonetics, MEGM SingleQuots #CC-4136). Spheres were cultured as follow: single cells were plated in ultralow attachment plates (Corning) at a density of 2x104 viable cells/ml in DMEM/F-12 medium supplemented with insulin (Clonetics, MEGM SingleQuots #CC-4136), EGF (Clonetics, MEGM SingleQuots #CC-4136), hydrocortisone (Clonetics, MEGM SingleQuots #CC-4136), B-27 Supplement (gibco # 17504044), 20 ng/ml human FGF-basic (PeproTech #100-18B) and 5 μg/ml heparin (Sigma-Aldrich #H3149). Formed mammospheres were collected after 6 days.

extract_protocol: Total RNAs were extracted from log-phase cells with TRIzol (Ambion #15596018), according to the manufacturer’s instructions.

treatment_protocol: IMECs and IMEC-MYC were maintained in DMEM/F-12 medium (gibco #11320-074) supplemented with insulin (Clonetics, MEGM SingleQuots #CC-4136), EGF (Clonetics, MEGM SingleQuots #CC-4136), bovine pituitary extract (BPE) (Clonetics, MEGM SingleQuots #CC-4136) and hydrocortisone (Clonetics, MEGM SingleQuots #CC-4136). Spheres were cultured in DMEM/F-12 medium supplemented with insulin (Clonetics, MEGM SingleQuots #CC-4136), EGF (Clonetics, MEGM SingleQuots #CC-4136), hydrocortisone (Clonetics, MEGM SingleQuots #CC-4136), B-27 Supplement (gibco # 17504044), 20 ng/ml human FGF-basic (PeproTech #100-18B) and 5 μg/ml heparin (Sigma-Aldrich #H3149).

value: non-transformed human mammary epithelial cells

tag: gender

value: female

tag: cell fraction


title: M2_clone#3

description:
SAMPLE 17
replicate 1

source_name: hTERT-immortalized human mammary epithelial cells


title: GFP+_1

description:
SAMPLE 10
replicate 1

value: GFP+


title: GFP-_2

description:
SAMPLE 14
replicate 2

value: GFP-


title: Huh7-hNTCP HDV infected in the presence of Myrcludex B

description:
10006031040_A_Grn
SAMPLE 3
Chip B

value: day 9 post-infection

value: No

value: Yes

value: concentration (ng/ml):85.9


title: GFP+_2

description:
SAMPLE 11
replicate 2


title: M2_2

description:
SAMPLE 8
replicate 2


title: M2_clone#2

description:
SAMPLE 16
replicate 1


title: GFP-_1

description:
SAMPLE 13
replicate 1


title: HuH7-hNTCP not infected

description:
10006031032_K_Grn
SAMPLE 1
Chip A

source_name: Huh7-hNTCP not infected

value: concentration (ng/ml):93.6


title: IMEC WT_3

description:
SAMPLE 3
replicate 3

value: IMEC WT


title: IMEC MYC_2

description:
SAMPLE 5
replicate 2

value: IMEC MYC


title: M2_clone#4

description:
SAMPLE 18
replicate 1


title: GFP+_3

description:
SAMPLE 12
replicate 3


title: HuH7-hNTCP HDV infected

description:
10006031032_L_Grn
SAMPLE 2
Chip A

source_name: Huh7-hNTCP HDV infected

value: concentration (ng/ml):153.8


title: IMEC MYC_1

description:
SAMPLE 4
replicate 1


title: M2_1

description:
SAMPLE 7
replicate 1


title: IMEC WT_1

description:
SAMPLE 1
replicate 1


title: IMEC MYC_3

description:
SAMPLE 6
replicate 3


title: IMEC WT_2

description:
SAMPLE 2
replicate 2


title: 391_TP1_SS6_3_1 (batch 7)

type: genomic

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a iScan+ System (Illumina).

data_processing: Genomic DNA extracted from biopsies and individual crypts was genotyped using Illumina Omni 2.5M SNP Array. File normalized_data.txt reports Log.R.Ratio and B.Allele.Freq.

molecule: genomic DNA

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (WG-MSM) and primer/neutralization mix (WG-RPM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Biopsies: Genomic DNA from fresh frozen biopsies was isolated using PureLink Genomic DNA Mini Kit (Invitrogen/Life Technologies) Crypts: Genomic DNA from individual Barrett's crypts was obtained by lysis of in TE + proteinase K.

tag: patient

tag: progressor

value: progressor


title: 391_TP1_SS6_3_2 (batch 7)


title: 391_TP1_SS6_2_2 (batch 7)


title: 391_TP2_73P_normal_5350N_5ng (batch 7)

source_name: Blood


title: 391_TP1_SS6_4_1 (batch 7)


title: 852_TP2_A14_4_1 (batch 7)


title: 740_TP1_SS6_3_2 (batch 7)


title: 852_TP2_A14_3_1 (batch 7)


title: 740_TP1_SS6_4_2 (batch 7)


title: 740_TP1_SS6_2_2 (batch 7)


title: 740_TP1_SS6_3_1 (batch 7)


title: 852_TP2_A14_2_2 (batch 7)


title: 848_TP1_SS9_4_2 (batch 7)


title: 740_TP2_5O_normal_8102N_5ng (batch 7)


title: 852_TP1_normal_19684N_5ng (batch 7)


title: GFP-_3

description:
SAMPLE 15
replicate 3


title: 848_TP1_SS9_4_1 (batch 7)


title: 852_TP2_A14_3_2 (batch 7)


title: 848_TP1_SS9_3_1 (batch 7)


title: 848_TP1_SS9_1_2 (batch 7)


title: 848_TP1_SS9_2_2 (batch 7)


title: 740_TP1_SS6_4_1 (batch 7)


title: 848_TP1_SS9_whole_epi (batch 7)


title: 911_TP1_SS6_whole_epi (batch 7)

value: non-progressor


title: 911_TP2_SS8_whole_epi (batch 7)


title: 848_TP1_SS9_1_1 (batch 7)


title: 911_TP1_normal_10397N_5ng (batch 7)


title: 911_TP2_SS5_whole_epi (batch 7)


title: 848_TP1_SS1_normal_18780N_200ng (batch 7)


title: 911_TP1_SS4_whole_epi (batch 7)


title: 848_TP1_SS9_2_1 (batch 7)


title: 911_TP2_SS5_3_2 (batch 7)


title: 911_TP2_SS5_2_1 (batch 7)


title: 911_TP2_SS5_2_2 (batch 7)


title: 911_TP2_SS5_3_1 (batch 7)


title: 848_TP1_SS1_normal_18780ND_5ng (batch 7)


title: 911_TP2_SS5_4_2 (batch 7)


title: 911_TP2_SS5_4_1 (batch 7)


title: 911_TP1_SS6_4_1 (batch 7)


title: 911_TP1_SS6_2_2 (batch 7)


title: 848_TP1_SS9_3_2 (batch 7)


title: 911_TP2_SS5_1_1 (batch 7)


title: 911_TP1_SS6_2_1 (batch 7)


title: 911_TP2_SS3_whole_epi (batch 7)


title: 911_TP1_SS6_3_2 (batch 7)


title: 911_TP2_SS3_4_1 (batch 7)


title: 911_TP1_SS6_3_1 (batch 7)


title: 911_TP1_SS10_whole_epi (batch 7)


title: 911_TP1_normal_10397N_200ng (batch 7)


title: 911_TP2_SS5_1_2 (batch 7)


title: 911_TP1_SS6_4_2 (batch 7)


title: 911_TP1_SS6_1_2 (batch 7)


title: 911_TP2_SS3_2_2 (batch 7)


title: 911_TP2_SS3_2_1 (batch 7)


title: 911_TP2_SS3_1_2 (batch 7)


title: 911_TP2_SS3_1_1 (batch 7)


title: 911_TP1_SS6_1_1 (batch 7)


title: 852_TP2_A16_whole_epi (batch 6)

description: 852__A16_whole epi__22192


title: 852_TP2_A14_whole_epi (batch 6)

description: 852__A14_whole epi__22789


title: 852_TP2_A13_whole_epi (batch 6)

description: 852__A13_whole epi__22187


title: 852_TP2_A4_whole_epi (batch 6)

description: 852__A4_whole epi__22189


title: 852_TP2_B8_whole_epi (batch 6)

description: 852__B8_whole epi__22193


title: 852_TP1_normal_19684N_5ng (batch 6)


title: 852_TP1_SS2_4_1 (batch 6)


title: 911_TP2_SS3_3_2 (batch 7)


title: 852_TP1_SS13_whole_epi (batch 6)

description: 852_113M_SS13_whole epi__22184


title: 852_TP1_SS2_whole_epi (batch 6)

description: 852_113M_SS2_whole epi__22185


title: 911_TP2_SS8_4_2 (batch 7)


title: 911_TP2_SS3_4_2 (batch 7)


title: 852_TP2_A14_2_1 (batch 6)


title: 852_TP1_normal_19684N_200ng (batch 6)


title: 852_TP2_A14_1_1 (batch 6)


title: 852_TP1_SS2_2_1 (batch 6)


title: 852_TP1_SS2_1_1 (batch 6)


title: 852_TP2_A14_1_2 (batch 6)


title: 852_TP2_B8_3_2 (batch 6)


title: 391_TP1_SS6_4_2 (batch 7)


title: 852_TP1_SS2_4_2 (batch 6)


title: 852_TP2_A3_whole_epi (batch 6)

description: 852__A3_whole epi__22186


title: 852_TP2_A16_4_2 (batch 6)


title: 852_TP2_A6_whole_epi (batch 6)

description: 852__A6_whole epi__22191


title: 852_TP2_B8_1_1 (batch 6)


title: 852_TP2_B6_whole_epi (batch 6)

description: 852__B6_whole epi__22190


title: 852_TP1_SS2_2_2 (batch 6)


title: 852_TP2_A16_4_1 (batch 6)


title: 911_TP2_SS3_3_1 (batch 7)


title: 852_TP1_SS8_whole_epi (batch 6)

description: 852_113M_SS2_whole epi__22648


title: 911_TP2_SS8_4_1 (batch 7)


title: 852_TP1_SS2_3_3 (batch 6)


title: 852_TP2_A16_3_2 (batch 6)


title: 852_TP2_B8_4_2 (batch 6)


title: 852_TP2_A16_1_2 (batch 6)


title: 852_TP1_SS2_1_3 (batch 6)


title: 852_TP2_A6_4_1 (batch 6)


title: 852_TP2_A14_4_2 (batch 7)


title: 852_TP2_A6_2_1 (batch 6)


title: 852_TP2_A6_1_1 (batch 6)


title: 852_TP2_B6_4_2 (batch 6)


title: 852_TP2_B6_3_1 (batch 6)


title: 852_TP2_B6_4_1 (batch 6)


title: 852_TP2_A16_3_1 (batch 6)


title: 852_TP2_B8_3_1 (batch 6)


title: 852_TP2_B8_2_3 (batch 6)


title: 852_TP2_B8_2_1 (batch 6)


title: 852_TP2_A16_2_1 (batch 6)


title: 852_TP2_A16_1_1 (batch 6)


title: 852_TP1_SS2_3_2 (batch 6)


title: 852_TP2_B8_1_2 (batch 6)


title: 852_TP2_A6_2_2 (batch 6)


title: 852_TP2_B6_2_1 (batch 6)


title: 852_TP2_A6_3_1 (batch 6)


title: 852_TP2_A4_1_2 (batch 6)


title: 852_TP2_A4_2_1 (batch 6)


title: 852_TP2_A4_2_2 (batch 6)


title: 852_TP2_B6_3_2 (batch 6)


title: 852_TP2_B8_4_1 (batch 6)


title: 852_TP2_A4_1_1 (batch 6)


title: 852_TP2_A13_3_2 (batch 6)


title: 852_TP2_A13_4_1 (batch 6)


title: 852_TP2_A6_4_2 (batch 6)


title: 852_TP2_A13_2_1 (batch 6)


title: 852_TP2_A4_3_1 (batch 6)


title: 852_TP2_A3_4_2 (batch 6)


title: 852_TP2_A4_4_1 (batch 6)


title: 852_TP2_A16_2_2 (batch 6)


title: 852_TP2_A6_1_2 (batch 6)


title: 852_TP2_B6_1_1 (batch 6)


title: 852_TP1_SS8_3_1 (batch 6)


title: 852_TP1_SS8_2_3 (batch 6)


title: 852_TP2_B6_1_2 (batch 6)


title: 852_TP2_B6_2_2 (batch 6)


title: 852_TP1_SS8_2_2 (batch 6)


title: 852_TP2_A6_3_2 (batch 6)


title: 852_TP1_SS13_4_2 (batch 6)


title: 852_TP1_SS13_3_2 (batch 6)


title: 852_TP2_A13_4_2 (batch 6)


title: 852_TP2_A3_1_1 (batch 6)


title: 852_TP2_A4_3_2 (batch 6)


title: 852_TP2_A13_2_2 (batch 6)


title: 852_TP2_A13_1_1 (batch 6)


title: 852_TP1_SS13_2_2 (batch 6)


title: 852_TP1_SS13_3_1 (batch 6)


title: 852_TP1_SS13_1_2 (batch 6)


title: 391_TP2_73P_normal_5350N_5ng (batch 5)


title: 391_TP2_73P_normal_5350N_200ng (batch 5)


title: 852_TP2_A3_3_1 (batch 6)


title: 852_TP2_A3_3_2 (batch 6)


title: 391_TP2_A3_whole_epi (batch 5)

description: 391_175R_A3_whole epi__22333


title: 852_TP2_A13_3_1 (batch 6)


title: 852_TP2_A3_4_1 (batch 6)


title: 391_TP2_C2_whole_epi (batch 5)

description: 391_175R_C2_whole epi__22331


title: 391_TP2_B4_whole_epi (batch 5)

description: 391_175R_B4_whole epi__22328


title: 852_TP1_SS13_4_1 (batch 6)


title: 852_TP2_A4_4_2 (batch 6)


title: 852_TP2_A3_2_1 (batch 6)


title: 852_TP2_A3_2_2 (batch 6)


title: 852_TP1_SS8_4_2 (batch 6)


title: 391_TP2_C3_whole_epi (batch 5)

description: 391_175R_C3_whole epi__22329


title: 852_TP1_SS8_1_2 (batch 6)


title: 852_TP2_A3_1_2 (batch 6)


title: 852_TP2_A13_1_2 (batch 6)


title: 391_TP1_SS8_whole_epi (batch 5)

description: 391_62K_SS8_whole epi__22324


title: 852_TP1_SS8_4_1 (batch 6)


title: 852_TP1_SS8_3_2 (batch 6)


title: 391_TP1_SS6_1_2 (batch 5)


title: 391_TP1_SS6_1_1 (batch 5)


title: 852_TP1_SS13_1_1 (batch 6)


title: 391_TP2_B2_whole_epi (batch 5)

description: 391_175R_B2_whole epi__22332


title: 391_TP2_A4_whole_epi (batch 5)

description: 391_175R_A4_whole epi__22330


title: 391_TP1_SS6_whole_epi (batch 5)

description: 391_67K_SS6_whole epi__22662


title: 391_TP2_C4_whole_epi (batch 5)

description: 391_175R_C4_whole epi__22327


title: 852_TP1_SS13_2_1 (batch 6)


title: 391_TP1_SS6_2_1 (batch 5)


title: 391_TP1_SS4_whole_epi (batch 5)

description: 391_62K_SS4_whole epi__22325


title: 391_TP2_A3_4_1 (batch 5)


title: 391_TP2_A3_3_2 (batch 5)


title: 391_TP2_B2_4_2 (batch 5)


title: 391_TP2_A3_1_1 (batch 5)


title: 391_TP2_B2_4_1 (batch 5)


title: 391_TP2_B2_2_3 (batch 5)


title: 391_TP2_A5_whole_epi (batch 5)

description: 391_175R_A5_whole epi__22326


title: 391_TP2_A3_1_3 (batch 5)


title: 391_TP2_B2_2_1 (batch 5)


title: 391_TP2_A3_2_2 (batch 5)


title: 391_TP2_C2_4_2 (batch 5)


title: 391_TP2_B2_1_2 (batch 5)


title: 391_TP2_B2_1_1 (batch 5)


title: 391_TP2_A3_2_1 (batch 5)


title: 391_TP2_C2_3_2 (batch 5)


title: 391_TP2_C2_4_1 (batch 5)


title: 391_TP2_C2_3_1 (batch 5)


title: 391_TP2_C2_1_1 (batch 5)


title: 391_TP2_C2_2_1 (batch 5)


title: 391_TP2_C2_2_2 (batch 5)


title: 391_TP2_A3_4_2 (batch 5)


title: 391_TP2_A4_4_3 (batch 5)


title: 391_TP2_C2_1_2 (batch 5)


title: 391_TP2_A4_3_2 (batch 5)


title: 391_TP2_A4_4_2 (batch 5)


title: 852_TP1_SS8_1_1 (batch 6)


title: 391_TP2_A4_2_2 (batch 5)


title: 391_TP2_A3_3_1 (batch 5)


title: 391_TP2_A4_1_1 (batch 5)


title: 391_TP2_C3_4_2 (batch 5)


title: 391_TP2_A4_3_1 (batch 5)


title: 391_TP2_A4_1_3 (batch 5)


title: 391_TP2_C3_1_2 (batch 5)


title: 391_TP2_B2_2_2 (batch 5)


title: 391_TP2_B4_4_1 (batch 5)


title: 391_TP2_B4_3_2 (batch 5)


title: 391_TP2_C3_3_1 (batch 5)


title: 391_TP2_B4_3_1 (batch 5)


title: 391_TP2_C3_3_2 (batch 5)


title: 391_TP2_C3_2_2 (batch 5)


title: 391_TP2_B4_1_2 (batch 5)


title: 391_TP2_A4_2_1 (batch 5)


title: 391_TP2_B4_2_2 (batch 5)


title: 391_TP2_C4_3_1 (batch 5)


title: 391_TP2_C3_2_1 (batch 5)


title: 391_TP2_B4_2_1 (batch 5)


title: 391_TP2_C4_3_2 (batch 5)


title: 391_TP2_C4_4_2 (batch 5)


title: 391_TP2_C4_2_1 (batch 5)


title: 391_TP2_C4_1_2 (batch 5)


title: 391_TP2_B4_1_3 (batch 5)


title: 391_TP2_C4_2_2 (batch 5)


title: 391_TP2_A5_4_2 (batch 5)


title: 391_TP2_B4_4_2 (batch 5)


title: 391_TP2_A5_2_2 (batch 5)


title: 391_TP2_C3_4_1 (batch 5)


title: 391_TP2_A5_3_2 (batch 5)


title: 391_TP2_C3_1_1 (batch 5)


title: 391_TP2_C4_4_1 (batch 5)


title: 391_TP2_C4_1_1 (batch 5)


title: 391_TP2_A5_1_2 (batch 5)


title: 391_TP2_A5_4_1 (batch 5)


title: 391_TP2_A5_3_1 (batch 5)


title: 391_TP2_A5_1_1 (batch 5)


title: 391_TP1_SS4_4_1 (batch 5)


title: 391_TP1_SS4_3_1 (batch 5)


title: 391_TP1_SS4_3_2 (batch 5)


title: 391_TP1_SS4_4_2 (batch 5)


title: 391_TP1_SS4_2_2 (batch 5)


title: 391_TP1_SS4_2_1 (batch 5)


title: 391_TP1_SS4_1_2 (batch 5)


title: 391_TP1_SS4_1_1 (batch 5)


title: 391_TP2_A5_2_1 (batch 5)


title: 391_TP1_SS8_1_2 (batch 5)


title: 391_TP1_SS8_1_1 (batch 5)


title: 391_TP1_SS8_4_1 (batch 5)


title: 740_TP2_5O_normal_8102N_200ng (batch 4)


title: 391_TP1_SS8_3_1 (batch 5)


title: 740_TP2_B4_whole_epi (batch 4)

description: 740__B4_whole epi__22052


title: 740_TP2_5O_normal_8102N_5ng (batch 4)


title: 740_TP2_C3_whole_epi (batch 4)

description: 740__C3_whole epi__22050


title: 391_TP1_SS8_3_2 (batch 5)


title: 740_TP1_SS4_whole_epi (batch 4)

description: 740_78M_SS4_whole epi__22045


title: 740_TP1_SS7_whole_epi (batch 4)

description: 740_78M_SS7_whole epi__22044


title: 740_TP1_SS6_whole_epi (batch 4)

description: 740_78M_SS6_whole epi__22634


title: 391_TP1_SS8_2_1 (batch 5)


title: 740_TP2_A4_whole_epi (batch 4)

description: 740__A4_whole epi__22051


title: 391_TP1_SS8_2_2 (batch 5)


title: 740_TP2_C4_4_2 (batch 4)


title: 740_TP2_A3_whole_epi (batch 4)

description: 740__A3_whole epi__22049


title: 740_TP2_A2_whole_epi (batch 4)

description: 740__A2_whole epi__22046


title: 740_TP2_C4_3_1 (batch 4)


title: 740_TP2_C4_2_1 (batch 4)


title: 740_TP2_C4_2_2 (batch 4)


title: 740_TP2_C4_1_1 (batch 4)


title: 391_TP1_SS8_4_2 (batch 5)


title: 740_TP2_C4_whole_epi (batch 4)

description: 740__C4_whole epi__22053


title: 740_TP2_B2_whole_epi (batch 4)

description: 740__B2_whole epi__22047


title: 740_TP1_SS6_2_1 (batch 4)


title: 740_TP2_A4_4_2 (batch 4)


title: 740_TP2_C4_1_2 (batch 4)


title: 740_TP1_SS6_1_1 (batch 4)


title: 740_TP2_A4_3_2 (batch 4)


title: 740_TP2_A4_2_2 (batch 4)


title: 740_TP2_A4_2_1 (batch 4)


title: 740_TP2_C2_whole_epi (batch 4)

description: 740__C2_whole epi__22048


title: 740_TP2_B4_4_2 (batch 4)


title: 740_TP2_B4_1_2 (batch 4)


title: 740_TP2_C4_4_1 (batch 4)


title: 740_TP2_C3_4_1 (batch 4)


title: 740_TP2_A4_4_1 (batch 4)


title: 740_TP2_B4_4_1 (batch 4)


title: 740_TP2_C3_3_2 (batch 4)


title: 740_TP2_C3_2_2 (batch 4)


title: 740_TP2_C3_2_1 (batch 4)


title: 740_TP2_B4_3_2 (batch 4)


title: 740_TP2_B4_1_1 (batch 4)


title: 740_TP2_C3_1_2 (batch 4)


title: 740_TP2_A3_4_1 (batch 4)


title: 740_TP2_A3_3_2 (batch 4)


title: 740_TP1_SS6_1_2 (batch 4)


title: 740_TP2_C3_4_3 (batch 4)


title: 740_TP2_B4_3_1 (batch 4)


title: 740_TP2_A4_1_2 (batch 4)


title: 740_TP2_A3_2_1 (batch 4)


title: 740_TP2_A4_1_1 (batch 4)


title: 740_TP2_B4_2_1 (batch 4)


title: 740_TP2_A4_3_1 (batch 4)


title: 740_TP2_C2_4_1 (batch 4)


title: 740_TP2_B4_2_2 (batch 4)


title: 740_TP2_C2_4_2 (batch 4)


title: 740_TP2_C2_3_1 (batch 4)


title: 740_TP2_C4_3_2 (batch 4)


title: 740_TP2_C3_3_1 (batch 4)


title: 740_TP2_A3_3_1 (batch 4)


title: 740_TP2_C3_1_1 (batch 4)


title: 740_TP2_C2_1_1 (batch 4)


title: 740_TP2_A3_4_2 (batch 4)


title: 740_TP2_B2_4_1 (batch 4)


title: 740_TP2_B2_2_2 (batch 4)


title: 740_TP2_C2_2_2 (batch 4)


title: 740_TP2_A3_1_1 (batch 4)


title: 740_TP2_A3_1_2 (batch 4)


title: 740_TP2_B2_2_1 (batch 4)


title: 740_TP2_B2_1_1 (batch 4)


title: 740_TP2_B2_3_1 (batch 4)


title: 740_TP2_B2_1_2 (batch 4)


title: 740_TP2_A2_4_1 (batch 4)


title: 740_TP2_C2_2_1 (batch 4)


title: 740_TP2_A3_2_2 (batch 4)


title: 740_TP2_B2_3_2 (batch 4)


title: 740_TP2_A2_3_2 (batch 4)


title: 740_TP2_A2_1_2 (batch 4)


title: 740_TP2_A2_2_1 (batch 4)


title: 740_TP1_SS4_4_2 (batch 4)


title: 740_TP2_C2_3_2 (batch 4)


title: 740_TP1_SS4_3_1 (batch 4)


title: 740_TP2_A2_3_1 (batch 4)


title: 740_TP2_B2_4_2 (batch 4)


title: 740_TP2_A2_2_2 (batch 4)


title: 740_TP1_SS4_2_2 (batch 4)


title: 740_TP1_SS4_4_1 (batch 4)


title: 740_TP1_SS7_3_2 (batch 4)


title: 740_TP1_SS4_3_3 (batch 4)


title: 740_TP2_C2_1_2 (batch 4)


title: 740_TP1_SS7_3_1 (batch 4)


title: 740_TP1_SS7_2_1 (batch 4)


title: 740_TP2_A2_4_2 (batch 4)


title: 740_TP2_A2_1_1 (batch 4)


title: 740_TP1_SS4_1_2 (batch 4)


title: 740_TP1_SS4_2_1 (batch 4)


title: 740_TP1_SS4_1_1 (batch 4)


title: 740_TP1_SS7_4_2 (batch 4)


title: 740_TP1_SS7_2_2 (batch 4)


title: 911_TP2_SS8_1_1 (batch 3)


title: 911_TP2_SS8_2_2 (batch 3)


title: 911_TP2_SS8_1_2 (batch 3)


title: 740_TP1_SS7_4_1 (batch 4)


title: 911_TP1_normal_10397N_5ng (batch 3)


title: 740_TP1_SS7_1_2 (batch 4)


title: 911_TP2_SS8_3_1 (batch 3)


title: 911_TP1_SS4_3_2 (batch 3)


title: 391_TP2_B2_3_3 (batch 5)


title: 911_TP1_SS4_2_2 (batch 3)


title: 911_TP1_SS4_1_2 (batch 3)


title: 911_TP2_SS8_3_2 (batch 3)


title: 911_TP1_SS4_4_2 (batch 3)


title: 911_TP1_SS4_3_1 (batch 3)


title: 911_TP2_SS8_2_1 (batch 3)


title: 911_TP1_SS4_4_1 (batch 3)


title: 911_TP1_SS10_4_2 (batch 3)


title: 911_TP1_SS4_1_1 (batch 3)


title: 911_TP1_SS10_2_2 (batch 3)


title: 740_TP1_SS7_1_1 (batch 4)


title: 911_TP1_SS10_1_2 (batch 3)


title: 911_TP1_SS10_2_1 (batch 3)


title: 911_TP1_SS10_3_2 (batch 3)


title: 911_TP1_SS10_1_1 (batch 3)


title: 911_TP1_SS4_2_1 (batch 3)


title: 256_TP2__normal_354N_5ng (batch 3)


title: 256_TP1_SS15_whole_epi (batch 3)

description: 256_106P_SS15_whole epi_22744


title: 911_TP1_SS10_3_3 (batch 3)


title: 256_TP2_SS6_whole_epi (batch 3)

description: 256_42Y_SS6_whole epi_22507


title: 911_TP1_SS10_4_1 (batch 3)


title: 256_TP1_SS18_1_1 (batch 3)


title: PPRV Infected cells_replicate1

city: Karnal

first: Ravi Kumar

last: Gandham

state: Haryana

address: Makrampur

country: India

institute: ICAR-NBAGR

description:
G268_R1_0617
PBMCs collected at 9 day post infection from infected group

data_processing:
fastq files containing sequencing reads, each of control and infected samples were imported to CLC Workbench 6.1 software, where in, adapters were trimmed  from the reads. Thereafter, known miRNAs were identified by annotating the clean reads according to miRBase 11 (Bos taurus species). The counts obtained were analyzed using edgeR for identifying differentially expressed miRNAs under PPPRV infection.
Supplementary_files_format_and_content: tab-delimited text files include miRNA name,  expression values (log2 fold change) and significant p-value

organism: Capra hircus

source_name: PPRV Infected cells

extract_protocol:
Total RNA from each of the collected samples was isolated using the RNeasy Mini kit (Qiagen GmbH, Germany) according to the manufacturer’s protocol. The integrity and quantity of isolated RNA were assessed on a Bioanalyzer (Agilent Technologies, Inc). The RNA integrity number (RIN) value of all the samples was found greater than 8, which is considered suitable for further processing.
Library was prepared using NEBNext Multiplex Small RNA Library Prep Kit (New England Biolabs Inc.) following the manufacturer’s protocol. The quality of the libraries was assessed on Bioanalyzer and quantification was done using a Qubit 2.0 Fluorometer (Life Technologies) and by quantitative real-time PCR. Libraries wee sequenced on Illumina – NextSeq500  following manufacturer’s protocol.

treatment_protocol: Two groups of PBMCs including control and PPRV (Izatnagar/94-virulent strain) infected were used in the study. From both the groups blood was collected was collected and PBMCs were isloated at 9 day post infection. The isolated PBMCs of both groups were collected in RNase free 1.5 ml centrifuge tube in RNA later.

tag: infected with

value: PPRV (Izatnagar/94-virulent strain)

value: PBMCs


title: 256_TP2__normal_354N_200ng (batch 3)


title: 256_TP1_SS18_whole_epi (batch 3)

description: 256_106P_SS18_whole epi_22504


title: 256_TP2_SS18_whole_epi (batch 3)

description: 256_42Y_SS18_whole epi_22506


title: 256_TP2_SS12_4_2 (batch 3)


title: 256_TP2_SS12_whole_epi (batch 3)

description: 256_42Y_SS12_whole epi_22745


title: 256_TP2_SS12_3_2 (batch 3)


title: root 24h DEX 3

city: Wageningen

first: Jules

last: Beekwilder

address: Droevendaalsesteeg 1

institute: Wageningen Plant Research

description: root 24h DEX 3

data_processing:
De-multiplexing of obtained sequences was done using CASAVA 1.8.1. software.
Reads were mapped with CLC Genomics Workbench 8.0 (Qiagen)
Genome_build: Solanum lycopersicon ITAG2.4
Supplementary_files_format_and_content: reads were mapped on the tomato genome version ITAG2.4 (gene models). Gene expression ratios for DEX samples compared to control samples were determined for each timepoint
" processed data.xlsx".  The columns in this file called " raw CLC output" provide ratios between expression levels: so column D: callus 3h DEX/callus control; column E: callus 24h DEX/callus control; column F: root 3h DEX/root control; column G: root 24h DEX/root control.

organism: Solanum lycopersicum

source_name: root

growth_protocol: ambient temperature, 16h light, 8h dark

extract_protocol:
RNeasy plant minikit (Qiagen)
TruSeq Stranded mRNA Sample Preparation Protocol (Illumina)
Equimolar amounts of libraries were pooled and diluted towards 6pM concentrations for paired end clustering on one lanes of a flow cell V4 (Illumina) and analyzed paired end on a HiSeq2500 instrument using a 126,7,126 flow cycle pattern.

treatment_protocol: Dexamethason was added to a concetration of 10 mg/L

tag: agent

value: induced with DEX

value: root

tag: time point


title: root 24h DEX 1

description: root 24h DEX 1


title: root 24h DEX 2

description: root 24h DEX 2


title: PBMCs Control_replicate1

description:
G267_R1_0617
PBMCs collected at 9 day post infection from control group

source_name: PBMCs Control

value: none (control)


title: root 3h DEX 3

description: root 3h DEX 3


title: root 3h DEX 2

description: root 3h DEX 2


title: 256_TP2_SS12_2_2 (batch 3)


title: 256_TP2_SS12_4_1 (batch 3)


title: PBMCs Control_replicate2

description:
G502_S15_R1_001
PBMCs collected at 9 day post infection from control group


title: 256_TP2_SS12_1_1 (batch 3)


title: 256_TP1_SS12_whole_epi (batch 3)

description: 256_106P_SS12_whole epi_22505


title: 256_TP1_SS15_4_1 (batch 3)


title: 256_TP1_SS15_3_2 (batch 3)


title: PPRV Infected cells_replicate2

description:
G603_S16_R1_001
PBMCs collected at 9 day post infection from infected group, replicate2


title: 256_TP1_SS15_3_1 (batch 3)


title: callus 24h DEX 1

description: callus 24h DEX 1

source_name: callus

value: callus


title: callus 3h DEX 2

description: callus 3h DEX 2


title: 256_TP1_SS15_2_1 (batch 3)


title: root control 3

description: root control 3

value: not induced


title: 256_TP2_SS12_1_2 (batch 3)


title: root control 2

description: root control 2


title: 256_TP2_SS6_4_2 (batch 3)


title: 256_TP2_SS12_3_1 (batch 3)


title: root control 1

description: root control 1


title: callus control 1

description: callus control 1


title: 256_TP2_SS12_2_1 (batch 3)


title: 256_TP1_SS15_4_2 (batch 3)


title: 256_TP2_SS6_3_1 (batch 3)


title: callus 24h DEX 3

description: callus 24h DEX 3


title: callus 24h DEX 2

description: callus 24h DEX 2


title: 256_TP1_SS15_2_2 (batch 3)


title: root 3h DEX 1

description: root 3h DEX 1


title: 256_TP1_SS15_1_2 (batch 3)


title: callus 3h DEX 3

description: callus 3h DEX 3


title: 256_TP2_SS6_3_2 (batch 3)


title: 256_TP2_SS18_4_3 (batch 3)


title: callus control 2

description: callus control 2


title: callus control 3

description: callus control 3


title: E18.5 WT mouse lung, MOE430B

city: Halifax

first: Boris

last: Kablar

state: Nova Scotia

address: 5850 College Street

department: Medical Neuroscience

country: Canada

institute: Dalhousie University

description: Gene expression data from wild-type fetal lung.

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

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

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

source_name: E18.5 mouse lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: fetal lung

value: BALB/c

tag: age


title: 256_TP2_SS18_3_2 (batch 3)


title: 256_TP2_SS18_4_1 (batch 3)


title: 256_TP2_SS18_2_2 (batch 3)


title: 256_TP2_SS6_4_1 (batch 3)


title: 256_TP1_SS15_1_1 (batch 3)


title: E18.5 WT mouse lung, MOE430A


title: 256_TP2_SS18_2_1 (batch 3)


title: 256_TP2_SS6_2_1 (batch 3)


title: callus 3h DEX 1

description: callus 3h DEX 1


title: E18.5 Myf5-/-:MyoD-/- mouse lung, MOE430A

description: Gene expression data from double knock-out (MyoD-/-:Myf5-/-) fetal lung.

value: BALB/c Myf5:Myod null


title: 256_TP2_SS18_1_1 (batch 3)


title: 256_TP2_SS6_2_2 (batch 3)


title: 256_TP1_SS12_4_2 (batch 3)


title: 256_TP2_SS18_1_2 (batch 3)


title: 256_TP2_SS6_1_2 (batch 3)


title: 256_TP1_SS12_3_2 (batch 3)


title: 256_TP2_SS18_3_1 (batch 3)


title: 256_TP2_SS6_1_1 (batch 3)


title: 256_TP1_SS12_3_1 (batch 3)


title: ER_E2_90min_4_Input

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

country: United Kingdom

institute: University of York

library_source: genomic

data_processing:
Aligment with BWA
DAC Blacklisted
Peaks called with MACS
Full R Markdown avalible at https://github.com/andrewholding/VULCANSupplementary
Genome_build: Hg19 for ER, GRChr38 for GRHL2

growth_protocol: MCF7 were grown in stripped media for 5 days before treatment

extract_protocol:
Cells were cross-linked with 1% Formaldhye, DNA was sheared using ultrasound and IP was overnight at 4C
ThruPLEX

value: Breast

tag: chip-antibody

value: Input


title: GRHL2_Ctrl_2_Input


title: ER_Ctrl_4_Input


title: GRHL2_E2_45min_1_Input


title: E18.5 Myf5-/-:MyoD-/- mouse lung, MOE430B


title: 256_TP1_SS12_2_1 (batch 3)


title: E13.5 MyoD-/- mouse limb muscle

description: Gene expression data from MyoD-/- knock-out fetal limb muscle.

source_name: E13.5 mouse limb muscle

value: fetal limb muscle

value: BALB/c Myod null


title: E13.5 WT mouse limb muscle

description: Gene expression data from wild-type fetal limb muscle.


title: 256_TP1_SS12_1_1 (batch 3)


title: 256_TP1_SS12_1_2 (batch 3)


title: 256_TP1_SS18_4_3 (batch 3)


title: E13.5 Myf5-/- mouse back muscle

description: Gene expression data from Myf5-/- knock-out fetal back muscle.

source_name: E13.5 mouse back muscle

value: fetal back muscle

value: BALB/c Myf5 null


title: ER_E2_90min_2_Input


title: GRHL2_E2_45min_2_Input


title: ER_Ctrl_2_Input


title: ER_E2_90min_1_Input


title: E13.5 WT mouse back muscle

description: Gene expression data from wild-type fetal back muscle.


title: GRHL2_Ctrl_3_Input


title: E18.5 WT mouse palate

description: Gene expression data from wild-type fetal palate.

source_name: E18.5 mouse palate

value: fetal palate


title: ER_E2_45min_4_Input


title: GRHL2_Ctrl_1_Input


title: 437_TP2_SS6_whole_epi (batch 3)

description: 437_90W_SS6_whole epi_22717

value: non-progressor


title: GRHL2_E2_45min_3_Input


title: ER_E2_45min_2_Input


title: GRHL2_E2_45min_1


title: 256_TP1_SS12_2_2 (batch 3)


title: ER_E2_45min_3_Input


title: 437_TP1_normal_18096N_200ng (batch 3)


title: 437_TP1_normal_18096N_5ng (batch 3)


title: 256_TP1_SS12_4_1 (batch 3)


title: 256_TP1_SS18_3_1 (batch 3)


title: E18.5 Myf5-/-:MyoD-/- mouse palate

description: Gene expression data from double knock-out (MyoD-/-:Myf5-/-) fetal palate.


title: GRHL2_Ctrl_2


title: 437_TP2_SS4_whole_epi (batch 3)

description: 437_90W_SS4_whole epi_22451


title: ER_Ctrl_3_Input


title: 437_TP2_SS9_whole_epi (batch 3)

description: 437_90W_SS9_whole epi_22450


title: GRHL2_Ctrl_1


title: 437_TP1_SS3_whole_epi (batch 3)

description: 437_44P_SS3_whole epi_22449


title: GRHL2_Ctrl_3


title: 437_TP2_SS6_4_2 (batch 3)


title: ER_E2_45min_3


title: ER_E2_45min_1_Input


title: ER_E2_90min_3


title: 256_TP1_SS18_3_2 (batch 3)


title: 256_TP1_SS18_2_2 (batch 3)


title: 256_TP1_SS18_1_2 (batch 3)


title: ER_Ctrl_1_Input


title: 437_TP1_SS7_whole_epi (batch 3)

description: 437_44P_SS7_whole epi_22716


title: ER_E2_90min_4


title: 256_TP1_SS18_4_2 (batch 3)


title: ER_E2_45min_2


title: 256_TP1_SS18_2_1 (batch 3)


title: ER_E2_90min_1


title: ER_Ctrl_2


title: 437_TP2_SS6_1_3 (batch 3)


title: GRHL2_E2_45min_3


title: ER_E2_45min_1


title: 437_TP2_SS6_1_2 (batch 3)


title: GRHL2_E2_45min_2


title: ER_E2_90min_3_Input


title: HCC1806 spheroid rep3

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

description:
HCC1806P2230
cell grown in DMEM/Nutrient Mixture F-12 Ham

data_processing:
Quality control with FastQC v 0.11.6
Mappping was done using STAR v 2.5.0 and RSEM v 1.3.0.
Genome_build: mm10 and hg19 UCSC annotation
Supplementary_files_format_and_content: tab delimited, including transcript counts, FPKM and TPM

growth_protocol: Cells grown in RPMI-1640 supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich) and Penicillin/Streptomycin solution at 1x dilution (Sigma-Aldrich) (bulk)

extract_protocol:
Total RNA was isolated from 2 x 10^6 cells ausing the TriZol reagent (Thermo-Fisher Scientific) and following manufacturer’s instructions.
Libraries for RNA sequencing were generated using TruSeq RNA sample preparation kit v2 (Illumina Inc., San Diego, CA, USA) following manufacturer’s instructions, using 1 µg of total RNA as input material and 15 PCR cycles for DNA amplification. Libraries were quantified by Qubit 2.0 Fluorometer using ds DNA High Sensitivity Qubit Assay (Thermo-Fisher Scientific) and pooled together in equimolar amounts.

treatment_protocol: Cells grown in DMEM/Nutrient Mixture F-12 Ham (Sigma-Aldrich) supplemented with 0.4% bovine serum albumin (BSA, Sigma-Aldrich), 20 ng/mL bFGF (PeproTech EC Ltd., London, UK), 20 ng/mL EGF (Sigma-Aldrich) and 5 µg/mL insulin (Sigma-Aldrich).  (spheroids)

value: Triple-negative breast cancer (TNBC)


title: 437_TP1_normal_18096N_5ng (batch 2)


title: 437_TP1_SS7_3_1 (batch 2)


title: HCC1806 bulk rep2

description:
HCC1806E224A
cell grown in RPMI-1640


title: ER_Ctrl_4


title: 437_TP1_SS7_2_1 (batch 2)


title: 437_TP1_SS7_1_3 (batch 2)


title: HCC1806 bulk rep1

description:
HCC1806E224B
cell grown in RPMI-1640


title: 437_TP2_SS6_3_1 (batch 3)


title: 437_TP1_SS7_1_2 (batch 2)


title: 437_TP2_SS4_4_3 (batch 2)


title: ER_Ctrl_3


title: 437_TP1_SS7_4_2 (batch 3)


title: 437_TP2_SS4_4_2 (batch 2)


title: 437_TP1_SS7_2_2 (batch 2)


title: 437_TP2_SS4_2_1 (batch 2)


title: 437_TP1_SS12_whole_epi (batch 3)

description: 437_44P_SS12_whole epi_22448


title: 437_TP2_SS4_1_2 (batch 2)


title: HCC1806 bulk rep3

description:
HCC1806E224C
cell grown in RPMI-1640


title: 437_TP2_SS6_2_2 (batch 3)


title: ER_E2_90min_2


title: ER_E2_45min_4


title: 437_TP2_SS4_3_1 (batch 2)


title: 437_TP2_SS6_2_1 (batch 3)


title: HCC1806 spheroid rep2

description:
HCC1806P2232B
cell grown in DMEM/Nutrient Mixture F-12 Ham


title: 437_TP2_SS9_4_3 (batch 2)


title: 437_TP2_SS6_3_2 (batch 3)


title: 437_TP2_SS9_2_1 (batch 2)


title: 437_TP2_SS9_2_2 (batch 2)


title: 437_TP2_SS4_3_2 (batch 2)


title: 437_TP2_SS4_2_2 (batch 2)


title: 437_TP2_SS9_1_1 (batch 2)


title: 437_TP1_SS7_3_2 (batch 2)


title: HCC1806 spheroid rep1

description:
HCC1806P2232A
cell grown in DMEM/Nutrient Mixture F-12 Ham


title: 437_TP1_SS7_4_1 (batch 2)


title: 437_TP2_SS9_3_1 (batch 2)


title: ER_Ctrl_1


title: 437_TP2_SS4_1_1 (batch 2)


title: 437_TP2_SS6_4_1 (batch 3)


title: 437_TP1_SS3_3_2 (batch 2)


title: 437_TP2_SS9_4_1 (batch 2)


title: 437_TP1_SS3_4_2 (batch 2)


title: 437_TP1_SS3_1_2 (batch 2)


title: 437_TP2_SS9_3_2 (batch 2)


title: 437_TP1_SS3_3_1 (batch 2)


title: 437_TP2_SS9_1_2 (batch 2)


title: 437_TP1_SS3_4_1 (batch 2)


title: 437_TP1_SS3_1_1 (batch 2)


title: 437_TP1_SS3_2_3 (batch 2)


title: 437_TP1_SS12_3_3 (batch 2)


title: 437_TP1_SS3_2_1 (batch 2)


title: Long-range VIP-GABAergic cell from the VIP-eGFP mouse hippocampus s7

city: Quebec

first: Lisa

last: Topolnik

state: Quebec

department: Biochemistry, Microbiology and Bio-informatics

institute: Université Laval

description: cytoplasmic RNA, nuclear RNA

data_processing:
Sequencing raw data were de-multiplexed to discriminate reads from different samples and then trimmed to remove sequencing adapters, low confidence bases, sequencing-specific bias and PCR artifacts. We computed reads alignments as a measure of quality, specifically the fraction of reads that could be mapped back to the mouse genome (mm10 assembly) as indicated by the aligner STAR (v2.5.2a). For reads quantification we computed pseudo-alignments using Kallisto (Pachter Lab, UC Berkeley). The average number of pseudo-aligned reads per cell was 2.1 million.
Genome_build: mm10
Supplementary_files_format_and_content: 7 tab excel files containing 1 sample per tab with target_id, eff_length, est_counts, tpm and gene name.

source_name: Long-range VIP-GABAergic cell from the mouse hippocampus

growth_protocol: mice housed in 12hr day light cycle, fed ad libitum

extract_protocol:
acute hippocampal slices in ACSF, patch-clamp recordings followed by cell mechanical aspiration, the cell content was extracted in the lysis buffer containing the RNAse inhibitor
The cDNA libraries were constructed using SMART-Seq v4 Ultra low input RNA Kit. cDNA from SMART sequences was amplified by PCR Primer II A. After 17 cycles of long-distance PCR, amplified cDNA was purified using the Agencourt AMPure XP Kit.The quality of cDNA library construction was validated using the Agilent Tapestation 2200 system. The threshold cDNA concentration of 200 pg/ml was achieved in all samples. cDNA libraries from 23 cells were prepared for Illumina Next Generation sequencing using Nextera XT DNA Library Preparation Kits. Libraries with unique index were then pooled together in equimolar ratio and sequenced for paired-end sequencing using both lanes of a rapid run flow-cell on the Illumina HiSeq 2500 system. The average insert size for the paired-end libraries was 225 base pairs.

treatment_protocol: no experimental treatment

value: VIP-eGFP (MMRRC strain #31009)

value: Hippocampus, CA1 area, stratum oriens/alveus

value: Long-range VIP-GABAergic cell


title: Long-range VIP-GABAergic cell from the VIP-eGFP mouse hippocampus s3

description: cytoplasmic RNA, nuclear RNA


title: Long-range VIP-GABAergic cell from the VIP-eGFP mouse hippocampus s5

description: cytoplasmic RNA, nuclear RNA


title: Kidney Col4a3-/-_2

city: Miami

first: Lina

last: Shehadeh

state: FL

department: Medicine

country: USA

institute: University of Miami

hyb_protocol: Affymetrix FlashTag Biotin HSR RNA Labeling Kit (P/N 901910)

scan_protocol: Command ConsoleTM User Guide (P/N 702569); GeneChip Scanner 3000 7G system; GeneChip Command Console Software (AGCC)

data_processing: Expression ratios were calculated in Genespring 13.0 as the power-2 exponential of the log2 differences. The acceptance criteria for gene array expression changes was a minimum 2 fold change in log2 (equivalent to 4 fold) and a one-way Analysis of Variance (ANOVA) t-test with Benjamini-Hochberg multiple testing correction p-value of <0.05.

label: FlashTag™ Biotin HSR RNA Labeling Reagent

source_name: Kindey tissue

extract_protocol: RNA was extracted from freshly snap frozen kidneys using Mirvana Paris kit.

treatment_protocol: Kidneys were snap frozen from 2 month old wild type (n=2), Col4a3-/- (n=3), or Col4a3-/-OPN-/- (n=3) mice. RNA was isolated using Mirvana Paris kit.

value: kidney


title: 437_TP1_SS12_4_1 (batch 2)


title: Long-range VIP-GABAergic cell from the VIP-eGFP mouse hippocampus s4

description: cytoplasmic RNA, nuclear RNA


title: Long-range VIP-GABAergic cell from the VIP-eGFP mouse hippocampus s6

description: cytoplasmic RNA, nuclear RNA


title: 437_TP1_SS12_4_3 (batch 2)


title: 437_TP1_SS12_2_1 (batch 2)


title: Long-range VIP-GABAergic cell from the VIP-eGFP mouse hippocampus s1

description: cytoplasmic RNA, nuclear RNA


title: Long-range VIP-GABAergic cell from the VIP-eGFP mouse hippocampus s2

description: cytoplasmic RNA, nuclear RNA


title: Kidney Wild Type_2

label_protocol: Affymetrix FlashTag Biotin HSR RNA Labeling Kit (P/N 901910)

value: Wild Type


title: 437_TP1_SS12_2_2 (batch 2)


title: Kidney Col4a3-/-_1


title: Kidney Col4a3-/-OPN-/-_2


title: Kidney Col4a3-/-_3


title: 437_TP1_SS12_3_1 (batch 2)


title: Kidney Col4a3-/-OPN-/-_1


title: Kidney Col4a3-/-OPN-/-_3


title: Kidney Wild Type_1


title: 451_TP1_normal_6784N_200ng (batch 2)


title: 451_TP2_SS6_whole_epi (batch 2)

description: 451_76Z_SS6_whole epi_22689


title: H1693

city: Dallas

first: Kimberly

last: Batten

state: TX

address: 5323 Harry Hines Blvd

department: Cell biology

institute: UT Southwestern Medical Center

description:
Raw data to be submitted to dbGaP
raw_counts_from_BCM_RNAseq.txt

data_processing:
raw counts were obtained using ht-seq count on BAM files generated by aligning trimmed PE fastq files to UCSC human genome version hg19 using tophat 2.0.12.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: NSCLC cell line

extract_protocol:
RNA was extracted using Qiagen’s RNeasy plus mini kit following manufacturer's protocol
Sequencing was run at Baylor College of Medicine (BCM) or GENEWIZ on Illumina HiSeq 2500, 2x150bp configuration. Samples from GENEWIZ are indicated by "_GW" suffix in the sample name

tag: histology

value: Adenocarcinoma

tag: 6-thio-dg status

value: Resistant

tag: sequencing facility

value: BCM


title: 437_TP1_SS12_1_1 (batch 2)


title: H1993


title: 451_TP2_SS7_whole_epi (batch 2)

description: 451_76Z_SS7_whole epi_22394


title: 451_TP1_SS4_whole_epi (batch 2)

description: 451_115T_SS4_whole epi_22393


title: H1819


title: 451_TP2_SS6_2_1 (batch 2)


title: HCC1195

value: Sensitive


title: 451_TP1_normal_6784N_5ng (batch 2)


title: 451_TP1_SS6_4_2 (batch 2)


title: 451_TP2_SS6_1_2 (batch 2)


title: 451_TP2_SS6_4_1 (batch 2)


title: 451_TP2_SS6_2_2 (batch 2)


title: H1993_2


title: H2086


title: 451_TP1_SS7_whole_epi (batch 2)

description: 451_115T_SS7_whole epi_22392


title: 451_TP2_SS6_1_1 (batch 2)


title: 451_TP1_SS6_3_2 (batch 2)


title: 451_TP1_SS6_whole_epi (batch 2)

description: 451_115T_SS6_whole epi_22688


title: HCC461


title: 451_TP2_SS6_3_2 (batch 2)


title: 451_TP1_SS6_4_1 (batch 2)


title: 437_TP1_SS12_1_2 (batch 2)


title: 451_TP2_SS6_3_1 (batch 2)


title: 451_TP2_SS4_whole_epi (batch 2)

description: 451_76Z_SS4_whole epi_22395


title: 451_TP1_SS6_3_1 (batch 2)


title: 451_TP1_SS6_2_2 (batch 2)


title: H820


title: HCC4006


title: 451_TP1_SS6_1_1 (batch 2)


title: H2122


title: H2087


title: 451_TP2_SS7_4_2 (batch 2)


title: 451_TP2_SS7_3_2 (batch 2)


title: 451_TP2_SS7_3_1 (batch 2)


title: 451_TP2_SS6_4_2 (batch 2)


title: Calu-3


title: 451_TP2_SS7_1_2 (batch 2)


title: H157

value: Squamous


title: 451_TP2_SS7_1_1 (batch 2)


title: 54_WT

city: Brisbane

last: Piper

address: St Lucia

institute: The University of QUeensland

data_processing:
Raw reads alligned to mouse genome using Tophat
Transcript levels quantified in HTSeq-count (overlap mode "union", strandedness "no") by mapping to known RefSeq (NCBI) protein coding sequences downloaded from UCSC table browser in GTF format
Differential gene expression analysis performed using DeSeq2
Genome_build: mm10

source_name: Hippocampal neural progenitor cells

extract_protocol:
Dentate gyri were dissected and dissociated according to standard protocol
Smart-seq 2, 12 cycles of amplifcation for nestin-creERT2 dataset, 13 cycles of amplification for dcx-creERT2 dataset

tag: strain

tag: wt or nfix ko

value: WT

tag: cre-driver


title: WKY Hypothalamus Female

city: Tokyo

first: Sabine

last: Gouraud

address: 3-10-2  Osawa, Mitaka

country: Japan

institute: International Christian University

description: gene expression in the hypothalamus of female WKY

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60ºC for 30 minutes with 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Rat GE 4x44K v3 (Agilent) Microarrays for 17 hours at 65ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ºC GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent Technologies Scanner G2505C) using one color scan setting for Rat GE 4x44K v3 array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028282_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as “IsSaturated ”, IsFeatNonUnifOL ”and “IsBGNonUnifOL ” were excluded from both samples. Features that were not flagged as both gIsWellAboveBG andgIsPosAndSignifin at least one condition were eliminated.

organism: Rattus norvegicus

source_name: WKY Hypothalamus Female

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng of pooled RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The tissues were homogenized in TRIzol reagent and stored at −80ºC before being processed. Total RNA from each sample were isolated according to the protocol supplied by the manufacturer (Life Technologies) and stored at −80ºC. The purity (260/230 and 260/280 ratio >1.7) and integrity (RIN > 7) for all total RNA samples were verified by using a Nanodrop1000 and a 2100 Bioanalyzer Agilent respectively. For each gender, 100 ng of total RNA from each rat were pooled together.

treatment_protocol: All animals were allowed to eat and drink ad libitum until the day of the tissue collection. Animals were killed by ether inhalation followed by decapitation. The brain was rapidly removed from the cranium, a block of dorsal part of medulla oblongata was isolated, placed on an ice-cold platform. The hypothalamus was dissected under a dissecting microscope, immediatly homogenized in Trizol and stored at -80ºC until processing. A single operator performed all dissections.

tag: tissue

value: Hypothalamus

value: female

value: 9 weeks

value: Wistar Kyoto (WKY)


title: 69_KO

value: KO


title: 19_WT


title: 451_TP2_SS7_4_1 (batch 2)

value: non-progressor


title: WKY NTS Male

description: gene expression in the NTS of male WKY

hyb_protocol: 1.65ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60ºC for 30 minutes with 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Rat GE 4x44K v3 (Agilent) Microarrays for 17 hours at 65ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ºC GE Wash buffer 2 (Agilent), then dried.

source_name: WKY NTS Male

treatment_protocol: All animals were allowed to eat and drink ad libitum until the day of the tissue collection. Animals were killed by ether inhalation followed by decapitation. The brain was rapidly removed from the cranium, a block of dorsal part of medulla oblongata was isolated, placed on an ice-cold platform. The NTS, located between 1.0 mm rostral and 0.5 mm caudal to the calamus scriptorius (CS) were dissected under a dissecting microscope, immediatly homogenized in Trizol and stored at -80ºC until processing. A single operator performed all dissections.

value: nucleus tractus solitarius (NTS)

value: male


title: HCC44

tag: cell line


title: WKY NTS Female

description: gene expression in the NTS of female WKY

source_name: WKY NTS Female

tag: gender


title: H1975


title: 451_TP2_SS4_3_1 (batch 2)


title: WKY Hypothalamus Male

description: gene expression in the hypothalamus of male WKY

source_name: WKY Hypothalamus Male


title: 90_KO


title: 451_TP1_SS6_2_1 (batch 2)


title: 451_TP2_SS4_2_2 (batch 2)


title: 71_KO


title: 264_KO


title: 451_TP1_SS6_1_2 (batch 2)


title: 451_TP2_SS4_4_2 (batch 2)


title: H125

value: Adenosquamous


title: HCC1897


title: H1651


title: 451_TP2_SS4_3_2 (batch 2)


title: 261_WT


title: Calu-6


title: 451_TP2_SS4_4_1 (batch 2)


title: HCC366


title: 451_TP2_SS4_1_2 (batch 2)


title: H2882

value: NSCLC


title: 451_TP1_SS4_4_1 (batch 2)


title: 16_WT


title: 249_WT


title: HCC2108


title: 247_WT


title: 451_TP2_SS7_2_1 (batch 2)


title: H1770

value: Neuroendocrine


title: 451_TP2_SS4_2_1 (batch 2)


title: H2347

value: Adenocarcinoma


title: 451_TP2_SS4_1_1 (batch 2)


title: 451_TP1_SS7_4_2 (batch 2)


title: 451_TP2_SS7_2_2 (batch 2)


title: 451_TP1_SS4_3_1 (batch 2)


title: 255_KO


title: 451_TP1_SS7_3_1 (batch 2)


title: 451_TP1_SS4_2_1 (batch 2)


title: 451_TP1_SS4_2_2 (batch 2)


title: 451_TP1_SS4_1_1 (batch 2)


title: H661

value: Large Cell


title: 253_KO


title: H2250

value: BCM


title: 451_TP1_SS4_3_2 (batch 2)


title: Calu-1

value: Epidermoid carcinoma

value: Sensitive


title: 451_TP1_SS4_4_2 (batch 2)


title: 451_TP1_SS4_1_2 (batch 2)


title: H1944


title: PC-9


title: 838_TP1_81O_sortednl_6077N (batch 1)


title: 848_TP1_SS1_normal_18780ND_5ng (batch 1)

source_name: Blood

value: progressor


title: H2172


title: HCC827


title: 451_TP1_SS7_2_1 (batch 2)


title: 322_TP1_117P_sortednl_5469N (batch 1)


title: 451_TP1_SS7_2_2 (batch 2)


title: H2073


title: 451_TP1_SS7_4_1 (batch 2)


title: 451_TP1_SS7_1_2 (batch 2)


title: HCC1359


title: 322_TP1_130U_sortedA (batch 1)


title: 848_TP2_B3_whole_epi (batch 1)

description: 848_Surgical_B3_whole epi_21907


title: 451_TP1_SS7_1_1 (batch 2)


title: 838_TP1_81O_sortedG1 (batch 1)


title: 451_TP1_SS7_3_2 (batch 2)


title: PBMC at Visit 12, ID 19

city: Aarhus

first: Martin

last: Tolstrup

state: DK

address: Palle Juul-Jensens Boulevard 99

department: Department of Clinical Medicine

country: Denmark

institute: Aarhus University

description: Gene Expression data from total PBMC's harvested from blood of patients known to be infected with HIV-1.

hyb_protocol: Affymetrix Human Transcriptome Array 2.0 ST arrays were hybridized according to recommendations using Affymetrix WT plus kit.

scan_protocol: GeneChips were scanned using the GeneTitan Scanner.

data_processing: CEL files were processed using Expression Console to produce CHP files. The CHP files were then used in Transcriptomic Analysis Console (TAC) analysing  the individual gene differential.

source_name: PBMCs from humans infected with HIV-1 4 weeks after total of 8 weeks of panobinostat dosing

label_protocol: One hundred ng of total RNA was processed and labelled in parallel with external control as described by manufacturer

extract_protocol: Total RNA was extracted from PBMCs lysed in PAX tubes using the protocol provided by the manufacturer.  Quality assessment was conducted using  a Nanodrop spectrophotometer (Thermo). Total RNA RIN values were between 7,5 and 9.

treatment_protocol: Fifteen patients infected with HIV-1 on fully suppressive ART was included in the clinical trial CLEAR. Each patient received 12 doses of 20 mg panobinostat with three doses given every other week for a total of 8 weeks. PBMCs fro gene expression analysis was samlpes at baseline, after 3 doses, 4 weeks after dosing and 6 months after dosing

tag: drug dosing

value: 4 week follow-up

value: Male


title: 848_TP2_C8_whole_epi (batch 1)

description: 848_Surgical_C8_whole epi_21913

tag: patient


title: PBMC at baseline, ID 19

source_name: PBMCs from humans infected with HIV-1 before dosing with panobinostat

value: Baseline


title: 848_TP2_A6_whole_epi (batch 1)

description: 848_Surgical_A6_whole epi_21909

tag: progressor


title: 848_TP2_A3_whole_epi (batch 1)

description: 848_Surgical_A3_whole epi_21906


title: 848_TP2_A8_whole_epi (batch 1)

description: 848_Surgical_A8_whole epi_21911


title: 848_TP2_C6_whole_epi (batch 1)

description: 848_Surgical_C6_whole epi_21910


title: 848_TP2_B8_whole_epi (batch 1)

description: 848_Surgical_B8_whole epi_21912


title: H1666


title: H23


title: HCC4017


title: H1792


title: 848_TP2_C3_whole_epi (batch 1)

description: 848_Surgical_C3_whole epi_21908


title: 848_TP1_SS1_normal_18780N_200ng (batch 1)


title: 848_TP1_SS14_whole_epi (batch 1)

description: 848_85O_SS14_whole epi_21904


title: H1373


title: 848_TP2_B8_4_1 (batch 1)


title: PBMC at Visit 13, ID 19

source_name: PBMCs from humans infected with HIV-1 6 months after total of 8 weeks of panobinostat dosing

value: 6 month follow-up


title: 848_TP2_B8_3_2 (batch 1)


title: PBMC at Visit 4, ID 19

source_name: PBMCs from humans infected with HIV-1 after three doses (20 mg oral) panobinostat

value: After 3 doses


title: 848_TP2_C8_4_2 (batch 1)


title: PBMC at Visit 4, ID 18


title: 848_TP2_C8_1_2 (batch 1)


title: 848_TP2_C8_4_1 (batch 1)


title: 848_TP2_C8_1_1 (batch 1)


title: H2258


title: PBMC at Visit 13, ID 18


title: 848_TP2_B8_2_2 (batch 1)


title: H920


title: 848_TP2_C8_2_2 (batch 1)


title: 848_TP2_B8_1_2 (batch 1)


title: 848_TP2_C8_3_1 (batch 1)


title: HCC2429


title: 848_TP2_B8_4_2 (batch 1)


title: 848_TP2_B8_1_1 (batch 1)


title: 848_TP2_A8_4_1 (batch 1)


title: PBMC at baseline, ID 17


title: 848_TP2_C8_3_2 (batch 1)


title: PBMC at Visit 12, ID 18


title: 848_TP2_B8_3_1 (batch 1)


title: 848_TP2_C8_2_1 (batch 1)


title: PBMC at Visit 13, ID 15


title: PBMC at baseline, ID 18


title: HCC4017_1_GW

value: GENEWIZ


title: H2073_2


title: 848_TP1_SS3_whole_epi (batch 1)

description: 848_85O_SS3_whole epi_21905


title: HCC4017_2_GW


title: 848_TP2_B8_2_1 (batch 1)


title: 848_TP2_A8_2_1 (batch 1)


title: PBMC at Visit 13, ID 17


title: 848_TP2_A8_3_2 (batch 1)


title: PBMC at Visit 12, ID 15


title: PBMC at baseline, ID 15


title: PBMC at Visit 4, ID 17


title: PBMC at Visit 12, ID 17


title: 848_TP2_A8_3_1 (batch 1)


title: 848_TP2_A8_4_2 (batch 1)


title: H2087_1_GW


title: 20M_ZT16_rep1

city: New Brunswick

first: William

middle: J.

last: Belden

state: NJ

address: 59 Dudley Rd

department: Animal Sciences

institute: Rutgers, The State University of New Jersey

data_processing:
Tophat - Cufflinks pipeline: RNA sequencing reads were aligned with TopHat (version 2.0.9). To aid the alignment, the zebrafish genome reference and the GTF file were downloaded from Ensembl GRCz10. Transcriptomes were assembled with Cufflinks (version 2.2.1). All transcripts information from Cufflinks was combined to create the new GTF by Cuffmerge (FPKM cutoff was default 0.05) and the differential gene analysis and discovery of new transcripts was performed by Cuffdiff.
Hisat - Stringtie2 pipleline: Hisat2 (version 2.0.1) was used to align RNA-seq reads with Zv10 reference genome and GTF file. New index of Zv10 was built by Hisat2. The zebrafish transcriptome created by Hisat2 was assembled and merged by stringtie(version 1.2.2) to generate the merged GTF file. In transcript merge usage of stringtie, minimum input transcript FPKM (-F) set as 0.1.
Genome_build: Danio rerio, GRCz10

organism: Danio rerio

source_name: brain

growth_protocol: 4 Month (M), 12 M and 20 M zebrafish were entrained under 12:12 light:dark cycles for one week prior to tissue removal.

extract_protocol:
Total RNA was extracted from zebrafish brain tissues by Trizol protocol. The RNA were sent Sulzberger Columbia Genome Center for cDNA library preparation and sequencing
Ribosomal RNA was depleted with RiboZero Gold (Illumina) and converted to cDNA with TruSeq Stranded Library Kit (Illumina)

value: 20 months

tag: harvest time

value: brain


title: 20M_ZT16_rep2


title: H2087_2_GW


title: 20M_ZT4_rep2


title: 848_TP2_A8_1_1 (batch 1)


title: H2086_2_GW

value: Resistant


title: H2086_1_GW

value: NSCLC


title: PBMC at Visit 4, ID 15


title: H1993_2_GW


title: PBMC at Visit 13, ID 14


title: 848_TP2_C6_4_1 (batch 1)


title: 848_TP2_C6_4_2 (batch 1)


title: H1993_1_GW


title: H1693_2_GW


title: H1819_2_GW


title: H1693_1_GW


title: 848_TP2_C6_3_1 (batch 1)


title: 848_TP2_A8_1_2 (batch 1)


title: 12M_ZT4_rep2

value: 12 months


title: 20M_ZT4_rep1


title: 848_TP2_A8_2_2 (batch 1)


title: 12M_ZT4_rep1


title: 4M_ZT16_rep2

value: 4 months


title: 124M_ZT16_rep1


title: 848_TP2_C6_2_2 (batch 1)


title: 848_TP2_C6_3_2 (batch 1)


title: PBMC at baseline, ID 14


title: 848_TP2_C6_1_2 (batch 1)


title: 4M_ZT16_rep1


title: PBMC at Visit 12, ID 14


title: 848_TP2_C6_1_1 (batch 1)


title: 4M_ZT4_rep2


title: 12M_ZT16_rep2


title: H1819_1_GW


title: 848_TP2_A6_4_2 (batch 1)


title: 20mon_ZT16_rep3

description: ChIPed DNA

data_processing:
The reads of H3K9me3 ChIP seq were mapped on zebrafish GRCz10 genome downloaded from Ensembl with Bowtie. Bam files of triplicates of each condition were processed by MACS2 (version 2.2.1) to call broad peaks (FDR ≤ 0.01).
Genome_build: GRCz10

extract_protocol:
Lysated are prepared in FA-lysis buffer (0.5% deoxycholate) with sonication. Histone-DNA complexes were isolated with H3K9me3 (abcam 8898) antibody. The ChIPed DNA sent for Duke genome center or Genewiz LLC for library preparation and sequencing.
50-bp single end reads

tag: antibody


title: PBMC at Visit 12, ID 12


title: 20mon_ZT16_rep2

description: ChIPed DNA


title: PBMC at baseline, ID 10


title: PBMC at Visit 4, ID 14


title: PBMC at Visit 13, ID 09


title: PBMC at Visit 13, ID 12


title: 848_TP2_A6_4_1 (batch 1)


title: 848_TP2_A6_3_2 (batch 1)


title: PBMC at Visit 12, ID 09


title: ChIPseq_control

description: ChIPed DNA

value: GFP antibody (from hybridoma)


title: 20mon_ZT4_rep3

description: ChIPed DNA


title: PBMC at Visit 4, ID 12


title: PBMC at baseline, ID 12


title: 4M_ZT4_rep1


title: 20mon_ZT16_rep1

description: ChIPed DNA


title: 20mon_ZT4_rep1

description: ChIPed DNA


title: 20mon_ZT4_rep2

description: ChIPed DNA


title: PBMC at Visit 4, ID 10


title: 848_TP2_A6_2_1 (batch 1)


title: PBMC at Visit 13, ID 10


title: 848_TP2_A6_2_2 (batch 1)


title: 848_TP2_A6_3_1 (batch 1)


title: 12mon_ZT16_rep3

description: ChIPed DNA


title: 848_TP2_C3_4_2 (batch 1)


title: 848_TP2_A6_1_1 (batch 1)


title: 848_TP2_A6_1_2 (batch 1)


title: 848_TP2_C3_3_2 (batch 1)


title: PBMC at Visit 13, ID 08


title: 12mon_ZT16_rep1

description: ChIPed DNA


title: PBMC at Visit 4, ID 09


title: PBMC at Visit 4, ID 08


title: 848_TP2_C3_4_1 (batch 1)


title: PBMC at Visit 12, ID 08


title: PBMC at baseline, ID 09


title: 12mon_ZT4_rep3

description: ChIPed DNA


title: 12mon_ZT4_rep1

description: ChIPed DNA


title: 4mon_ZT16_rep3

description: ChIPed DNA


title: 12mon_ZT16_rep2

description: ChIPed DNA


title: 848_TP2_C3_2_1 (batch 1)


title: 12mon_ZT4_rep2

description: ChIPed DNA


title: 848_TP2_C6_2_1 (batch 1)


title: 848_TP2_C3_3_1 (batch 1)


title: 848_TP2_C3_1_1 (batch 1)


title: 848_TP2_C3_1_2 (batch 1)


title: 848_TP2_C3_2_2 (batch 1)


title: PBMC at Visit 12, ID 07


title: PBMC at baseline, ID 08


title: 848_TP2_B3_4_1 (batch 1)


title: 848_TP2_B3_4_2 (batch 1)


title: 4mon_ZT16_rep2

description: ChIPed DNA


title: 4mon_ZT4_rep2

description: ChIPed DNA


title: 4mon_ZT4_rep3

description: ChIPed DNA


title: PBMC at Visit 12, ID 10


title: PBMC at baseline, ID 07


title: PBMC at Visit 13, ID 06


title: PBMC at Visit 4, ID 07


title: 848_TP2_B3_3_1 (batch 1)


title: 848_TP2_B3_2_2 (batch 1)


title: 4mon_ZT4_rep1

description: ChIPed DNA


title: 848_TP2_B3_2_1 (batch 1)


title: 4mon_ZT16_rep1

description: ChIPed DNA


title: 848_TP2_B3_3_2 (batch 1)


title: TRAPS T50M

city: Birmingham

first: Stephanie

middle: Rose

last: Harrison

address: Mindelson Way

institute: Queen Elizabeth Hospital Birmingham

description:
TRAPS dermal fibroblast from patient bearing T50M mutation
microRNA
T50M

data_processing: data was normalised manually using the raw Ct values exported from the RT-qPCR thermal cycler, using the ΔΔCt method, relative to the housekeeping gene U6. Fold change was then determined relative to the average level of expression of the housekeeping gene.

label: TaqMan probe

source_name: Human skin biopsy

label_protocol: Expression of 380 microRNAs was then quantified using TaqMan Low Density Array Card A, using the manufacturers protocols and reagents. Gene expression was normalised relative to the average expression of the housekeeping gene U6, which is measured across 4 separate wells on the 384-microRNA array card A.

growth_protocol: All biopsy samples were digested and grown beyond passage 5. TRAPS 50M and C88R were grown in Cellutions fibroblast media (Cambridge Biosciences, Cambridge, UK). The c472 TRAPS fibroblasts and all 3 healthy control samples were grown in Dubecco’s Modified Eagle Medium (DMEM) [Gibco (Life Technologies), Paisley, UK] supplemented with foetal bovine serum (FBS) (10%v/v), penicillin-streptomycin (1%v/v), and minimum essential medium (MEM) non-essential amino acids (1% v/v)

extract_protocol: RNA-derived cDNA from unstimulated cells was synthesized using MegaPlex RT Human Pool A v3.0. Expression of 380 microRNAs was then quantified using Applied Biosystems TaqMan  MicroRNA Array A (v2.0) [catalog number 4398965], according to the manufacturers protocol.

treatment_protocol: No treatments were applied prior to extraction of microRNA

tag: diagnosis

value: TRAPS

tag: tnfrsf1a mutation

tag: cell type

value: dermal fibroblasts

tag: passage

value: passage 5 or greater


title: TRAPS C88R

description:
TRAPS dermal fibroblast from patient bearing C88R mutation
microRNA
C88R


title: Healthy control 3

description:
healthy control dermal fibroblast sample 3
microRNA
HC3

value: healthy control


title: 848_TP2_B3_1_2 (batch 1)

value: progressor


title: Screen3-4round GFP positive

city: Shanghai

first: SHAN

last: JIN

address: Scientific Research Center 2901 Cao Lang Road, Jin Shan District, Shanghai, P.R.China

country: China

institute: FUDAN University

description: Double Lane Sequencing

data_processing:
The Trimmomatic-0.33 software was used to remove the double-end sequences respectively: the base with the tail mass less than 25 was removed; the 20bp sliding window was set at the same time and 1bp was moved with the average mass of the bases in the window not less than 25; A sequence of less than 80 bp in length.
High-quality double-stranded sequences were linked using flash-1.2.11 software, with the smallest overlap region of 10 bp and the overlap region bases not mismatched ( the mismatch rate was 0)
The forward and backward primersw were removed, leaving a sequence with a length of 5 bp or more.
Genome_build: Gecko V2.0
Supplementary_files_format_and_content: Scores represent different length of the sequence frequency

source_name: Jurakat Cells

growth_protocol: Cells were grown under standard laboratory conditions and stably transfected with CRISPR components.

extract_protocol:
Cells were sorted via flow cytometry, genomic DNA was extracted, and PCR for the sgRNA sequences was performed.
Illumina adaptors and barcodes were incorporated into the PCR primers.PCR amplified libraries were generated with independent barcodes to allow multiplexing. 50% PhiX DNA was included in the sequencing run, as low diversity libraries were expected.
qiagen_PCR

treatment_protocol: Cells were transduced with sgRNA lentivirus

tag: sample type

value: transduced sgRNAs pre-selection

value: Peripheral Blood

tag: disease

value: Acute T Cell Leukemia


title: PBMC at Visit 12, ID 06

value: 4 week follow-up

value: Male


title: Screen3-4round GFP Initial

description: Double Lane Sequencing


title: PBMC at Visit 13, ID 07

value: 6 month follow-up


title: PBMC at Visit 12, ID 05


title: 848_TP2_A3_4_2 (batch 1)


title: PBMC at Visit 4, ID 05

value: After 3 doses


title: 848_TP2_B3_1_1 (batch 1)


title: PBMC at Visit 12, ID 04


title: Screen2-4round GFP negative

description: Double Lane Sequencing


title: PBMC at Visit 13, ID 04


title: Screen3-4round GFP negative

description: Double Lane Sequencing


title: Healthy control 2

description:
healthy control dermal fibroblast sample 2
microRNA
HC2


title: PBMC at Visit 4, ID 06


title: PBMC at baseline, ID 06

value: Baseline


title: Healthy control 1

description:
healthy control dermal fibroblast sample 1
microRNA
HC1


title: Screen2-4round GFP positive

description: Double Lane Sequencing


title: PBMC at baseline, ID 05


title: 848_TP2_A3_4_1 (batch 1)


title: TRAPS c472

description:
TRAPS dermal fibroblast from patient bearing c472 mutation
microRNA
c472


title: Screen1-4round GFP positive

description: Double Lane Sequencing


title: 848_TP2_A3_3_1 (batch 1)


title: Screen1-4round GFP negative

description: Double Lane Sequencing


title: 848_TP2_A3_3_2 (batch 1)


title: 848_TP2_A3_2_2 (batch 1)


title: 848_TP2_A3_1_1 (batch 1)


title: 848_TP2_A3_2_1 (batch 1)


title: Screen1-4round GFP Initial

description: Double Lane Sequencing


title: 848_TP2_A3_1_2 (batch 1)


title: Ctrl3.section_B

city: Los Angeles

first: Safiyyah

last: Ziyad

state: CA

address: 621 Charles E. Young Drive, South

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: piece 2

data_processing:
Alignment of mRNA-seq reads was aligned to mm10 genome using STAR_2.5.3a.
Read counts per gene files were genereated using using --quantMode GeneCounts and ENSEMBL mouse GRCm38.88 gtf file from ENSEMBL website.
Read counts betweeen different samples were normalized with LIMMA package in R.
Genome_build: mm10
Supplementary_files_format_and_content: .csv read counts per gene

extract_protocol:
Spleens pieces were cut, transferred to microcentrifuge tubes, snap frozen immediately in liquid nitrogen, and stored at -80C until RNA extraction.  RLT buffer containing beta-mercaptoethanol was was used to lyse spleens, which were then homogenized.  Qiagen RNeasy kit was used to isolate total RNA.
Illumina TruSeq unstranded poly-A selection kit (Cat# RS-122-2001) was used to make library from 1ug of RNA.

tag: strain

tag: genotype

value: WT

value: spleen


title: Ctrl3.section_A

description: piece 1


title: Screen2-4round GFP Initial

description: Double Lane Sequencing


title: 848_TP1_SS3_2_2 (batch 1)

data_processing: Genomic DNA extracted from biopsies and individual crypts was genotyped using Illumina Omni 2.5M SNP Array. File normalized_data.txt reports Log.R.Ratio and B.Allele.Freq.

extract_protocol: Biopsies: Genomic DNA from fresh frozen biopsies was isolated using PureLink Genomic DNA Mini Kit (Invitrogen/Life Technologies) Crypts: Genomic DNA from individual Barrett's crypts was obtained by lysis of in TE + proteinase K.


title: PBMC at baseline, ID 04


title: 848_TP1_SS3_4_1 (batch 1)


title: Ctrl2.section_B

description: piece 2


title: PBMC at Visit 13, ID 05


title: PBMC at Visit 4, ID 02


title: PBMC at baseline, ID 02


title: PBMC at Visit 12, ID 02


title: PBMC at Visit 13, ID 02


title: 848_TP1_SS3_2_1 (batch 1)


title: 848_TP1_SS3_3_2 (batch 1)


title: PBMC at Visit 4, ID 04


title: 848_TP1_SS3_4_2 (batch 1)


title: 848_TP1_SS3_3_1 (batch 1)


title: 848_TP1_SS3_1_1 (batch 1)


title: Ctrl2.section_A

description: piece 1


title: Ctrl1.section_B

description: piece 2


title: 848_TP1_SS14_4_1 (batch 1)


title: 848_TP1_SS14_4_2 (batch 1)


title: 848_TP1_SS14_3_2 (batch 1)


title: M267.section_1

description: piece 1

value: VEC-Cre;SB Transposase; onc2


title: F262.section_2

description: piece 2


title: F262.section_1

description: piece 1


title: PBMC at Visit 4, ID 01


title: 848_TP1_SS3_1_3 (batch 1)


title: 848_TP1_SS14_2_2 (batch 1)


title: Ctrl1.section_A

description: piece 1


title: 848_TP1_SS14_1_1 (batch 1)


title: M267.section_2

description: piece 2


title: Ctrl C

source_name: Spleen

extract_protocol:
Spleens pieces were cut, transferred to microcentrifuge tubes, snap frozen immediately in liquid nitrogen, and stored at -80C until RNA extraction.  RLT buffer containing beta-mercaptoethanol was was used to lyse spleens, which were then homogenized.  Qiagen RNeasy kit was used to isolate total RNA.
Illumina TruSeq stranded poly-A selection kit (Cat# NP-202-1001) was used to make libraries from 50ng of RNA using the NeoPrep system.


title: 848_TP1_SS14_2_1 (batch 1)


title: PBMC at Visit 12, ID 01


title: PBMC at Visit 13, ID 01


title: M267


title: Embryos from eggs treated with 11-KT (1 uM)

city: Farmington

first: Mara

middle: H.

last: O'Brien

state: CT

address: 263 Farmington Ave.

department: Craniofacial Sciences

institute: University of Connecticut Health Center

hyb_protocol: The labeled, fragmented DNA was hybridized to the Zebrafish Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.7) and the Brainarray zebrafishdrentrezgcdf R package (version 14.0.0) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/entrezg.download/Zebrafish_Dr_ENTREZG_14.0.0.zip).

source_name: Embryos from eggs treated with 11-KT

label_protocol: Total RNA was used for biotin cRNA labeling according to the standard Affymetrix protocol.

growth_protocol: Embryos were collected following natural spawning, washed, and 100 eggs were placed in 20 x 100 mm culture plates with 50 mL of egg water.

treatment_protocol: Embryos were treated with chemical at 72-96 hours post fertilization and then sacrificed by removing water and quick-freezing on dry ice.

tag: treatment

value: 11-ketotestosterone (11-KT)

value: Embryos from eggs


title: PBMC at baseline, ID 01


title: Embryos from eggs treated with DDE (1uM)

description: DDE

source_name: Embryos from eggs treated with DDE

value: Dichlorodiphenyldichloroethylene (DDE)

tag: tissue


title: 848_TP1_SS14_1_2 (batch 1)

city: Lyon cedex 08

last: Martinez

institute: Cancer Research Centre of Lyon


title: Ctrl B


title: 848_TP1_SS14_3_1 (batch 1)


title: F270.section_1

description: piece 1


title: F270


title: sRNAseq_spt5l_rep2

status: Public on Jan 29 2018

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

description: sRNAseq in spt5l-1 (rep2)

data_processing:
Qseq files for small RNA-seq from the sequencer were demultiplexed and converted to fastq format with a customized script for downstream analysis. Raw AGO4 RIP-seq data were obtained from previously published datasets (GSM707686)55 . Reads were then trimmed for Illumina adaptors using Cutadapt (v 1.9.1) and mapped to the TAIR10 reference genome using Bowtie(v1.1.0) 51 allowing only one unique hit (-m 1) and zero mismatch.
Genome_build: tair10
Supplementary_files_format_and_content: bigwig tracks, tab delimited text file

organism: Arabidopsis thaliana

source_name: floral tissue

growth_protocol: All plants were grown on soil under long day conditions (16 hours light, 8 hours dark).  Inflorescence tissues with both floral buds and open flowers were collected and used for the GRO-seq procedure.

extract_protocol:
Total RNA was first extracted with Zymo Direct-zol RNA mini Prep kit (ZRC200687) followed by a size selection of RNA on a 15% Urea TBE Polyacrylamide gel (Invitrogen, EC6885BOX). Gels containing 15- to 30-nt were cut for small RNA library.
After gel elution, Illumina TruSeq Small RNA kit (RS-200-0012) was used for making small RNA library. Agilent D1000 ScreenTape (5067-5582) was then used for checking the size and quality of final libraries.

value: floral

tag: ecotype


title: Ctrl A


title: sRNAseq_col_rep2

description: sRNAseq in Col (rep2)

value: Wild type


title: sRNAseq_spt5l_rep1

description: sRNAseq in spt5l-1 (rep1)


title: F270.section_2

description: piece 2


title: F262


title: GROseq_ago469_D762A_rep1

description: GROseq in ago4/6/9/D762A (rep1)

data_processing:
Library strategy: GRO-seq
Qseq files from the sequencer were demultiplexed and converted to fastq format with a customized script for downstream analysis. For GRO-seq data, paired-end reads were first trimmed for Illumina adaptors and primers using Cutadapt (v 1.9.1). After trimming, reads less than 10bp long were removed with a customized Perl script. Paired-end reads were then separately aligned to the reference TAIR10 genome using Bowtie (v1.1.0) by allowing only unique hit (-m 1) and up to 3 mismatches (-v 3). Pair reads aligned to positions within 2000bp to each other were considered as correct read pairs using, and reads aligned to Watson or Crick strands were separated by a customized Perl script.
Genome_build: tair10
Supplementary_files_format_and_content: bigwig tracks, tab delimited text file

extract_protocol:
Approximately 10 grams of inflorescence and meristem tissue was collected from plants and immediate placed in ice cold grinding buffer (300 mM sucrose, 20 mM Tris, pH 8.0, 5 mM MgCl2, 5 mM KCl, 0.2% Triton X-100, 5 mM β-mercaptoethanol, 35% glycerol). Nuclei were isolated as described previously16. Briefly, samples were ground with an OMNI International General Laboratory Homogenizer at 4°C until well homogenized, filtered through a 250µm nylon mesh, 100µm nylon mesh, miracloth, and finally a 40µm cell strainer before being split into 50ml conical tubes.  Samples were spun for 10 minutes at 5250g, the supernatant was discarded, and the pellets were pooled and resuspended in 25ml of grinding buffer using a dounce homogenizer.  The wash step was repeated at least once more and nuclei were resuspended in 1ml of freezing buffer (50 mM Tris, pH 8.0, 5 mM MgCl2, 20% glycerol, 5 mM β-mercaptoethanol).Approximately 5x106 nuclei in 200 µl of freezing buffer were run-on in 3x GRO-reaction buffer 16 with. Reactions were stopped after 5 minutes to minimize run on length (~5-15 nts) while still incorporating brUTP by addition of 750 µl Trizol LS and RNA purified according to the manual. Without fragmentation or Terminator treatment, nascent RNA was enriched twice for BrU by αBrdU (Santa Cruz Biotechnology sc-32323AC) and immunoprecipitated as described in Hetzel et al. 2016.
Sequencing libraries were prepared from precipitated RNA using TruSeq Small RNA Library Prep kit following manufacturer instructions (Illumina). For GROseq in Col-0, nrpd1, nrpe1 and nrpd1/e1 double mutants, 14 cycles of PCR were used to amplify the libraries and the products ranging from 100 to 500bp were size selected by agarose gel. The libraries were sequenced on Illumina HiSeq 2000 platform by paired-end 100bp sequencing. For GROseq in spt5l, 14 cycles of PCR were used to amplify the libraries and the products were size selected by double SPRI bead purification (ratio of Ampure beads to library: 0.5:1 to 1.1:1).


title: GROseq_ago469_rep2

description: GROseq in ago4/6/9 (rep2)


title: GROseq_ago4_D762A_rep2

description: GROseq in ago4-4/D762A (rep2)

value: Ws


title: GROseq_ago4_D762A_rep1

description: GROseq in ago4-4/D762A (rep1)


title: SHR HYPO Male

description: gene expression in the hypothalamus of male SHR

hyb_protocol: 0.6ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60ºC for 30 minutes with 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Sureprint G3 Rat GE 8x60k v2 (Agilent) Microarrays for 17 hours at 65ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ºC GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for GE 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 074036_D_F_201506121) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as “IsSaturated”, “IsFeatNonUnifOL” and “IsBGNonUnifOL” were excluded from both samples. Features that were not flagged as both "gIsWellAboveBG" and "gIsPosAndSignif" in at least one condition were eliminated.

source_name: SHR Hypothalamus Male

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of pooled RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The tissues were homogenized in TRIzol reagent and total RNAs from each sample were isolated according to the protocol supplied by the manufacturer (Life Technologies) and stored at −80°C. The purity (260/230 and 260/280 ratio >1.7) and integrity (RIN > 7) for all total RNA samples were verified by using a Nanodrop1000 and a 2100 Bioanalyzer Agilent respectively. For each gender, 100 ng of total RNAs from each rat were pooled together

treatment_protocol: All animals were allowed to eat and drink ad libitum until the day of the tissue collection. Animals were killed by ether inhalation followed by decapitation. The brain was rapidly removed from the cranium and placed on an ice-cold platform. A block containing hypothalamus was dissected under a dissecting microscope and stored at -80 ºC until next processing. A single operator performed all dissections.

value: Hypothalamus

tag: gender

value: male

tag: age

value: 9 weeks old

value: SHR


title: Embryos from eggs treated with dieldrin+DDE (each 1 uM)

description: Dieldrin+DDE

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

value: dieldrin+DDE


title: SHR HYPO Female

description: gene expression in the hypothalamus of female SHR

source_name: SHR Hypothalamus Female

value: female

value: 9 weeks od


title: GROseq_Ws_rep1

description: GROseq in Ws (rep1)


title: GROseq_Ws_rep2

description: GROseq in Ws (rep2)


title: GROseq_ago4_4_Ws_rep2

description: GROseq in ago4-4 (rep2)


title: GROseq_spt5l_rep3

description: GROseq in spt5l (rep3)


title: GROseq_ago469_rep1

description: GROseq in ago4/6/9 (rep1)


title: Embryos from eggs treated with dieldrin (1 uM)

description: Dieldrin

source_name: Embryos from eggs treated with dieldrin

value: dieldrin


title: sRNAseq_col_rep1

description: sRNAseq in Col (rep1)


title: Embryos from eggs treated with DMSO (0.005%)

description: DMSO

source_name: Embryos from eggs treated with DMSO

value: dimethyl sulfoxide (DMSO)


title: FACS swap separate virus green sorted

city: Seattle

first: Jay

last: Shendure

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
Cells were transduced with GFP and BFP constructs each of which had a distinct linked barcode. This was done using a number of lentivirus production methods and controls to quantify the rate of template switching. Genomic DNA was extracted, the barcoded portion of the lentiviral construct was amplified and sequenced per the methods in our manuscript. This is the separately packaged virus  sorted on green.
facs_gfp_bfp_proportions.txt

data_processing:
Expression matrix files and BAM files were generated using the cellranger pipeline provided by 10X genomics using version 1.3.1 as described on the company website using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.
Barcodes and guide sequences were extracted from samples corresponding to barcode enrichment libraries as described in the methods of our manuscript.
Amplicon sequencing data from our FACS experiments was processed using FASTQ files and searching for relevant sequences in the amplicon.
Genome_build: hg19
Supplementary_files_format_and_content: Expression matrix files and BAM files were generated using the cellranger pipeline provided by 10X genomics using version 1.3.1 as described on the company website using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices provided here are those output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that go along with this file are provided as TSV files.

source_name: MCF10a cells

growth_protocol: MCF10a cells were cultured in DMEM/F12 (Invitrogen) supplemented with 10% FBS, 1% pen-strep, 10 ng/mL EGF, 1 µg/mL hydrocortisone, 5 µg/mL insulin and 100 ng/mL cholera toxin. K562 cells were cultured in RPMI 1640+L-Glutamine (Gibco),  supplemented with 10% fetal bovine serum (Rocky Mountain Biologicals) and 1% pen-strep (Gibco).

extract_protocol:
10X genomics V1 protocol as per manufacturer recommendations.
10X genomics V1 protocol as per manufacturer recommendations.

treatment_protocol: For samples with mock or doxorubicin treatment, after tranduction with the lentiviral library and crowth for 2-3 weeks, MCF10a cells were seeded in 10 cm plates plates at 1 x 106 cells per well, allowed to attach overnight and media replaced with MCF10A media alone (mock) or MCF10A media containing 500 (arrayed and pooled pLGB-scKO experiments) or 100 nM (pHAGE-scKO and CROP-seq experiments; we ultimately decided that this lower dose was more appropriate and likely to provide more robust signal) doxorubicin prepared from a 500 µM stock of doxorubicin (Sigma) in water. 24 hours after drug exposure untreated and doxorubicin treated cells were harvested by trypsinization, washed with PBS and used for downstream assays.

tag: cell line

value: MCF10a cells

value: Randomly immortalized breast epithelial cells


title: FACS swap pooled virus green sorted

description:
Cells were transduced with GFP and BFP constructs each of which had a distinct linked barcode. This was done using a number of lentivirus production methods and controls to quantify the rate of template switching. Genomic DNA was extracted, the barcoded portion of the lentiviral construct was amplified and sequenced per the methods in our manuscript. This is the separately packaged virus  sorted on blue.
facs_gfp_bfp_proportions.txt


title: GROseq_ago469_D762A_rep2

description: GROseq in ago4/6/9/D762A (rep2)


title: GROseq_ago469_wtAGO4_rep2

description: GROseq in ago4/6/9/wtAGO4 (rep2)


title: GROseq_ago469_wtAGO4_rep1

description: GROseq in ago4/6/9/wtAGO4 (rep1)


title: GROseq_col_rep5

description: GROseq in Col (rep5)


title: SHR NTS Female

description: gene expression in the NTS of female SHR

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 074036_D_F_201506121) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as “IsSaturated”, “IIsFeatNonUnifOL” and “IsBGNonUnifOL” were excluded from both samples. Features that were not flagged as both "gIsWellAboveBG" and "gIsPosAndSignif" in at least one condition were eliminated.

source_name: SHR NTS Female

value: NTS


title: CROP-seq Experiment Mock

description:
Data collected from mock and 100nm doxorubicin treated MCF10a cells treated with a CRISPR KO library of different tumor suppressors using a modified version of the CROP-seq method. Single-cell RNA-seq sample prep and library preparation was performed according to recommendations from 10X genomics documentation for their Version 1 protocol.
cs.m.matrix.mtx
cs.m.genes.tsv
cs.m.barcodes.tsv
cs.celldataset.rds
cs.cell_metadata.tsv

value: mock


title: Arrayed Screen Dox

description:
Data collected from 500nm doxorubicin treated MCF10a cells treated with a CRISPR KO library of different tumor suppressors. These included lentiviral libraries produced using both pooled and arrayed lentivirus production and vector that reuires linkage of an sgRNA with a distal barcode. Single-cell RNA-seq sample prep and library preparation was performed according to recommendations from 10X genomics documentation for their Version 1 protocol.
initial.matrix.mtx
initial.genes.tsv
initial.barcodes.tsv
initial.celldataset.rds
initial.cell_metadata.tsv

value: 500nm doxorubicin


title: Pooled Screen Mock

description:
Data collected from mock treated MCF10a cells treated with a CRISPR KO library of different tumor suppressors. These included lentiviral libraries produced using both pooled and arrayed lentivirus production and vector that reuires linkage of an sgRNA with a distal barcode. Single-cell RNA-seq sample prep and library preparation was performed according to recommendations from 10X genomics documentation for their Version 1 protocol.
initial.matrix.mtx
initial.genes.tsv
initial.barcodes.tsv
initial.celldataset.rds
initial.cell_metadata.tsv


title: SHR NTS Male

description: gene expression in the NTS of male SHR

source_name: SHR NTS Male


title: GROseq_ago4_wtAGO4_rep2

description: GROseq in ago4-4/wtAGO4 (rep2)

value: floral


title: GROseq_ago4_wtAGO4_rep1

description: GROseq in ago4-4/wtAGO4 (rep1)


title: FACS swap Mixed cells green sorted

description:
Cells were transduced with GFP and BFP constructs each of which had a distinct linked barcode. This was done using a number of lentivirus production methods and controls to quantify the rate of template switching. Genomic DNA was extracted, the barcoded portion of the lentiviral construct was amplified and sequenced per the methods in our manuscript. This is the mixed cell control sorted on green.
facs_gfp_bfp_proportions.txt


title: FACS swap separate virus blue sorted

description:
Cells were transduced with GFP and BFP constructs each of which had a distinct linked barcode. This was done using a number of lentivirus production methods and controls to quantify the rate of template switching. Genomic DNA was extracted, the barcoded portion of the lentiviral construct was amplified and sequenced per the methods in our manuscript. This is the pooled virus  sorted on green.
facs_gfp_bfp_proportions.txt


title: GROseq_col_rep6

description: GROseq in Col (rep6)

value: Wild type


title: FACS swap Mixed Cells blue sorted

description:
Cells were transduced with GFP and BFP constructs each of which had a distinct linked barcode. This was done using a number of lentivirus production methods and controls to quantify the rate of template switching. Genomic DNA was extracted, the barcoded portion of the lentiviral construct was amplified and sequenced per the methods in our manuscript. This is the mixed cell control sorted on blue.
facs_gfp_bfp_proportions.txt


title: FACS swap BFP only blue sorted

description:
Cells were transduced with GFP and BFP constructs each of which had a distinct linked barcode. This was done using a number of lentivirus production methods and controls to quantify the rate of template switching. Genomic DNA was extracted, the barcoded portion of the lentiviral construct was amplified and sequenced per the methods in our manuscript. This is the BFP only control sorted on blue
facs_gfp_bfp_proportions.txt


title: Tfam (L/L, cre) rep1

city: Bentley

first: Irina

last: Kuznetsova

address: Building 304, Kent Street

department: The Centre for Crop and Disease Management

institute: Curtin University

description:
55251 ko
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv

data_processing:
HISAT2 version 2.0.4 (hisat2 -p 8 –dat) was used to perform alignment of paired-end reads to the Mus Musculus reference genome (GRCm38). The output files were sorted and indexed with SAMtools version 1.3.1
StringTie version 1.2.4  (stringtie -p 18 -e -B) was applied to estimate transcripts abundance
prepDE.py (http://ccb.jhu.edu/software/stringtie/dl/prepDE.py) Python version 2.7.6 was used to extract raw counts
DESeq2 R package version 3.3.2 was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: gene_count_matrix_tfam_strain.csv (Raw counts)
DESeq2_results_tfam_strain.csv (DESeq2 results)

source_name: heart

growth_protocol: Total RNA isolated from hearts

extract_protocol: standard TruSeq library preparation

tag: strain background

tag: genotype/variation

value: Tfam (L/L, cre)


title: Tfam (L/L, cre) rep2

description:
55253 ko
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv


title: CROP-seq Experiment Dox

description:
Data collected from mock and 100nm doxorubicin treated MCF10a cells treated with a CRISPR KO library of different tumor suppressors using a modified version of the CROP-seq method. Single-cell RNA-seq sample prep and library preparation was performed according to recommendations from 10X genomics documentation for their Version 1 protocol.
cs.d.matrix.mtx
cs.d.genes.tsv
cs.d.barcodes.tsv
cs.celldataset.rds
cs.cell_metadata.tsv

value: 100nm doxorubicin


title: Tfam (L/L) rep3

description:
55263 wt
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv

value: Tfam (L/L)


title: Tfam (L/L, cre) rep5

description:
55265 ko
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv


title: FACS swap GFP only green sorted

description:
Cells were transduced with GFP and BFP constructs each of which had a distinct linked barcode. This was done using a number of lentivirus production methods and controls to quantify the rate of template switching. Genomic DNA was extracted, the barcoded portion of the lentiviral construct was amplified and sequenced per the methods in our manuscript. This is the GFP only control sorted on green
facs_gfp_bfp_proportions.txt


title: Tfam (L/L) rep2

description:
55259 wt
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv


title: GROseq_ago4_4_Ws_rep1

description: GROseq in ago4-4 (rep1)

value: Ws


title: FACS swap pooled virus blue sorted

description:
Cells were transduced with GFP and BFP constructs each of which had a distinct linked barcode. This was done using a number of lentivirus production methods and controls to quantify the rate of template switching. Genomic DNA was extracted, the barcoded portion of the lentiviral construct was amplified and sequenced per the methods in our manuscript. This is the pooled virus  sorted on blue.
facs_gfp_bfp_proportions.txt


title: Pooled Screen Dox


title: Tfam (L/L, cre) rep4

description:
55261 ko
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv


title: Tfam (L/L) rep1

description:
55257 wt
gene_count_matrix_tfam_strain.csv
DESeq2_results_tfam_strain.csv